7WY4
Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L-Phenylalanine in complex with Styrene
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3WSP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 293 | PEG8000, Magnesium Chloride, Tris-HCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.97 | α = 90 |
b = 126.65 | β = 90 |
c = 148.75 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 X 6M | 2019-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL45XU | 1 | SPring-8 | BL45XU |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.45 | 48.22 | 100 | 0.113 | 0.122 | 0.998 | 9.74 | 6.761 | 187448 | 24.687 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.45 | 1.49 | 99.9 | 1.677 | 1.83 | 0.634 | 1.27 | 6.263 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3WSP | 1.45 | 48.22 | 187448 | 9838 | 99.97 | 0.1451 | 0.1433 | 0.1792 | RANDOM | 19.671 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.7 | 1.18 | -0.48 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.44 |
r_dihedral_angle_4_deg | 17.014 |
r_dihedral_angle_3_deg | 12.93 |
r_dihedral_angle_1_deg | 6.597 |
r_angle_refined_deg | 1.527 |
r_rigid_bond_restr | 1.492 |
r_angle_other_deg | 1.433 |
r_chiral_restr | 0.084 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7316 |
Nucleic Acid Atoms | |
Solvent Atoms | 875 |
Heterogen Atoms | 420 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
MOLREP | phasing |