Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at SACLA
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 | 4Q0H | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | 4.95 | 298 | Sodium Acetate, Peg400, 2-methyl-2,4-pentanediol |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.57 | 52.05 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 96.22 | α = 90 |
b = 55.49 | β = 92.84 |
c = 71.63 | γ = 90 |
Symmetry |
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Space Group | C 1 2 1 |
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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 | 298 | CCD | MPCCD | | 2015-02-01 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | FREE ELECTRON LASER | SACLA BEAMLINE BL3 | 0.987 | SACLA | BL3 |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 2.2 | 71.54 | 100 | 0.976 | 0.119 | 5.62 | 81.2 | | 18818 | | | |
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 | 2.2 | 2.28 | 100 | | 0.677 | 0.68 | 24.1 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 4Q0H | 2.2 | 71.54 | 18389 | 956 | 100 | 0.18084 | 0.1821 | 0.19 | 0.2033 | 0.22 | RANDOM | 50.258 |
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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0.36 | | -0.76 | 0.44 | | -0.72 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 37.627 |
r_dihedral_angle_3_deg | 13.566 |
r_dihedral_angle_4_deg | 12.759 |
r_long_range_B_refined | 6.758 |
r_long_range_B_other | 6.757 |
r_dihedral_angle_1_deg | 6.216 |
r_scangle_other | 4.406 |
r_mcangle_it | 3.599 |
r_mcangle_other | 3.599 |
r_scbond_it | 2.593 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 37.627 |
r_dihedral_angle_3_deg | 13.566 |
r_dihedral_angle_4_deg | 12.759 |
r_long_range_B_refined | 6.758 |
r_long_range_B_other | 6.757 |
r_dihedral_angle_1_deg | 6.216 |
r_scangle_other | 4.406 |
r_mcangle_it | 3.599 |
r_mcangle_other | 3.599 |
r_scbond_it | 2.593 |
r_scbond_other | 2.592 |
r_mcbond_it | 2.196 |
r_mcbond_other | 2.191 |
r_angle_refined_deg | 1.287 |
r_angle_other_deg | 0.913 |
r_chiral_restr | 0.072 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
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 | 2328 |
Nucleic Acid Atoms | |
Solvent Atoms | 117 |
Heterogen Atoms | 47 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
CrystFEL | data reduction |
PHASER | phasing |
CrystFEL | data scaling |