6A2J
Crystal structure of heme A synthase from Bacillus subtilis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 7 | 293 | 30% PEG 600, 0.1M sodium chloride, 0.1M lithium sulfate, 0.1M sodium HEPES pH 7.4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.37 | 63.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.465 | α = 90 |
b = 90.465 | β = 90 |
c = 147.309 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 | 15 | PIXEL | DECTRIS PILATUS 6M | 2017-12-05 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 40 | CCD | RAYONIX MX300HE | 2017-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0 | SPring-8 | BL41XU |
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 1.0 | SPring-8 | BL44XU |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.2 | 29.031 | 99.9 | 0.126 | 0.14 | 0.997 | 8.02 | 5.242 | 22834 | 52.75 |
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 | 2.2 | 2.32 | 99.7 | 1.23 | 1.372 | 0.494 | 1.2 | 5.092 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MIRAS | FREE R-VALUE | 2.2 | 29.031 | 1.92 | 22824 | 1150 | 99.91 | 0.2076 | 0.2064 | 0.2287 | 0 | 58.5128 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.708 |
f_angle_d | 2.01 |
f_chiral_restr | 0.124 |
f_bond_d | 0.017 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2431 |
Nucleic Acid Atoms | |
Solvent Atoms | 32 |
Heterogen Atoms | 411 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XDS | data scaling |
SOLVE | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |