3TVZ
Structure of Bacillus subtilis HmoB
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | hanging drop | 8.5 | 293 | 28% PEG 4000, 0.2M Magnesium chloride, 0.1M Tris-Hcl pH8.5, hanging drop, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.799 | α = 90 |
b = 64.799 | β = 90 |
c = 392.591 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 270 | 2010-06-14 | M | MAD | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2010-05-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 0.97865 | SPring-8 | BL41XU |
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 0.97904 | SPring-8 | BL41XU |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2 | 50 | 100 | 34657 | 34657 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 2 | 48.74 | 34446 | 1736 | 99.84 | 0.1986 | 0.1959 | 0.251 | RANDOM | 42.15 |
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] | |
0.03 | 0.02 | 0.03 | -0.05 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.603 |
r_dihedral_angle_4_deg | 20.68 |
r_dihedral_angle_3_deg | 15.848 |
r_dihedral_angle_1_deg | 7.156 |
r_scangle_it | 4.065 |
r_scbond_it | 2.664 |
r_mcangle_it | 1.656 |
r_angle_refined_deg | 1.541 |
r_mcbond_it | 1.031 |
r_nbtor_refined | 0.314 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3434 |
Nucleic Acid Atoms | |
Solvent Atoms | 301 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
SOLVE | phasing |