X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7Y2A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.8 | 293 | 1.3 M sodium citrate, 50 mM Tris-HCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 40.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.847 | α = 90 |
b = 41.117 | β = 104.3 |
c = 72.095 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 90 | CCD | RAYONIX MX225-HS | 2019-07-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 6D | 0.97934 | PAL/PLS | 6D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | |||||
1 | 1.2 | 30 | 99.4 | 0.065 | 0.076 | 0.039 | 0.994 | 16.8 | 3.6 | 73861 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.2 | 1.22 | 95.1 | 0.31 | 0.375 | 0.208 | 0.853 | 3.7 | 2.9 |
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 | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.2 | 30 | 70188 | 3656 | 99.22 | 0.14684 | 0.14529 | 0.1458 | 0.17774 | 0.1788 | RANDOM | 13.55 |
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] | |
0.59 | -0.23 | -0.11 | -0.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 38.777 |
r_dihedral_angle_2_deg | 35.284 |
r_dihedral_angle_4_deg | 27.536 |
r_sphericity_bonded | 14.714 |
r_dihedral_angle_3_deg | 12.37 |
r_dihedral_angle_1_deg | 6.966 |
r_rigid_bond_restr | 5.406 |
r_scangle_other | 5.022 |
r_long_range_B_refined | 4.948 |
r_long_range_B_other | 4.667 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2049 |
Nucleic Acid Atoms | |
Solvent Atoms | 242 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |