4PXH
Structure of P450sky (CYP163B3), a cytochrome P450 from skyllamycin biosynthesis in complex with a peptidyl carrier protein domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4PWV | PDB ENTRY 4PWV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | 20% PEG3350, 0.15 M calcium acetate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.56 | 65.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 161.7 | α = 90 |
b = 161.7 | β = 90 |
c = 337.49 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
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 PILATUS 6M | 2013-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.00002 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.7 | 47.893 | 99.9 | 0.117 | 24.5 | 19.7 | 72148 | 72098 | 3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.7 | 3 | 100 | 0.661 | 5.6 | 19.9 |
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 | PDB ENTRY 4PWV | 2.7 | 47.893 | 68521 | 3577 | 100 | 0.21608 | 0.2145 | 0.24598 | RANDOM | 54.081 |
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] | |
1.04 | 0.52 | 1.04 | -1.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.957 |
r_dihedral_angle_3_deg | 13.681 |
r_dihedral_angle_4_deg | 12.099 |
r_dihedral_angle_1_deg | 4.311 |
r_angle_refined_deg | 0.87 |
r_scangle_it | 0.842 |
r_scbond_it | 0.492 |
r_mcangle_it | 0.333 |
r_mcbond_it | 0.173 |
r_chiral_restr | 0.058 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11443 |
Nucleic Acid Atoms | |
Solvent Atoms | 73 |
Heterogen Atoms | 213 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |