Human NOQ1 enzyme in its holo form by serial crystallography
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 8C9J | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | 8.5 | 293 | 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 20% polyethylene glycol (PEG) 3350 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.71 | 54.58 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 62 | α = 90 |
b = 108 | β = 90 |
c = 200 | γ = 90 |
Symmetry |
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Space Group | P 21 21 21 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 295 | PIXEL | PSI JUNGFRAU 4M | | 2023-02-18 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.072 | ESRF | ID29 |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | fixed target |
Fixed Target |
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Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
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1 | Small SOS chips | | | | | |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Split (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
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1 | 2.5 | 100 | 97.1 | 0.142 | 9.9 | 154.1 | | 41455 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 2.5 | 2.56 | | | 1.5 | | | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.5 | 100 | 41455 | 4581 | 97.12 | 0.20281 | 0.19873 | 0.21 | 0.23869 | 0.24 | RANDOM | 69.291 |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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0.01 | | | 0.08 | | -0.09 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 15.84 |
r_long_range_B_refined | 10.18 |
r_long_range_B_other | 10.179 |
r_mcangle_it | 8.428 |
r_mcangle_other | 8.427 |
r_scangle_other | 7.724 |
r_dihedral_angle_1_deg | 6.522 |
r_dihedral_angle_2_deg | 5.995 |
r_mcbond_it | 5.482 |
r_mcbond_other | 5.481 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 15.84 |
r_long_range_B_refined | 10.18 |
r_long_range_B_other | 10.179 |
r_mcangle_it | 8.428 |
r_mcangle_other | 8.427 |
r_scangle_other | 7.724 |
r_dihedral_angle_1_deg | 6.522 |
r_dihedral_angle_2_deg | 5.995 |
r_mcbond_it | 5.482 |
r_mcbond_other | 5.481 |
r_scbond_it | 4.95 |
r_scbond_other | 4.936 |
r_angle_refined_deg | 1.372 |
r_angle_other_deg | 0.462 |
r_chiral_restr | 0.064 |
r_bond_refined_d | 0.006 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
r_dihedral_angle_4_deg | |
r_nbd_refined | |
r_nbd_other | |
r_nbtor_refined | |
r_nbtor_other | |
r_xyhbond_nbd_refined | |
r_xyhbond_nbd_other | |
r_metal_ion_refined | |
r_metal_ion_other | |
r_symmetry_vdw_refined | |
r_symmetry_vdw_other | |
r_symmetry_hbond_refined | |
r_symmetry_hbond_other | |
r_symmetry_metal_ion_refined | |
r_symmetry_metal_ion_other | |
r_scangle_it | |
r_rigid_bond_restr | |
r_sphericity_free | |
r_sphericity_bonded | |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 8882 |
Nucleic Acid Atoms | |
Solvent Atoms | 75 |
Heterogen Atoms | 15 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
MOLREP | phasing |