7CZI
Structure of the CYP102A1 Haem Domain with N-{2-[4-(Trifluoromethoxy)phenoxy]}acetoyl-L-Phenylalanine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5XA3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 293 | PEG 8000, Magnesium Chloride, Tris-HCl, 0.5 % DMSO, 125 uM N-{2-[4-(Trifluoromethoxy)phenoxy]}acetoyl-L-Phenylalanine |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.752 | α = 90 |
b = 128.591 | β = 90 |
c = 148.871 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 100 | PIXEL | DECTRIS EIGER X 16M | 2018-11-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0000 | SPring-8 | BL41XU |
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 | 1.64 | 48.7 | 100 | 0.183 | 0.191 | 0.052 | 0.996 | 8.5 | 13.4 | 138691 |
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 | 1.64 | 1.67 | 100 | 3.008 | 3.123 | 0.837 | 0.675 | 1.1 | 13.8 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5XA3 | 1.64 | 48.7 | 131612 | 6970 | 99.93 | 0.1917 | 0.1904 | 0.2151 | RANDOM | 24.344 |
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] | |
0.21 | 1.25 | -1.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.601 |
r_dihedral_angle_4_deg | 15.665 |
r_dihedral_angle_3_deg | 13.606 |
r_dihedral_angle_1_deg | 6.877 |
r_angle_refined_deg | 1.654 |
r_angle_other_deg | 1.435 |
r_chiral_restr | 0.087 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.009 |
r_gen_planes_other | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7328 |
Nucleic Acid Atoms | |
Solvent Atoms | 716 |
Heterogen Atoms | 264 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |