3BVO
Crystal structure of human co-chaperone protein HscB
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.0031 M Sodium azide, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (16% PEG 3350, 0.050 M Lithium sulfate, 0.10 M PIPES pH 6.5), cryoprotected with 20% PEG 3350, 0.050 M Lithium sulfate, 0.10 M PIPES pH 6.5 in four steps up to 20% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.644 | α = 90 |
b = 32.581 | β = 105.24 |
c = 114.362 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | CCD | MARMOSAIC 300 mm CCD | Adjustable focusing mirrors in K-B geometry | 2007-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.97934 | APS | 23-ID-D |
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 | 3 | 47.75 | 96.7 | 0.086 | 10.054 | 6.3 | 9770 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3 | 3.11 | 79.8 | 0.342 | 3.022 | 4.3 | 780 |
Refinement
Statistics | |||||||||||||||||||
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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 | SAD | THROUGHOUT | 3 | 47.75 | 9242 | 753 | 97.489 | 0.24 | 0.236 | 0.288 | RANDOM | 72.562 |
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] | |
0.085 | -0.703 | 4.31 | -4.765 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.164 |
r_dihedral_angle_4_deg | 19.232 |
r_dihedral_angle_3_deg | 17.365 |
r_scangle_it | 5.666 |
r_dihedral_angle_1_deg | 5.06 |
r_scbond_it | 3.778 |
r_mcangle_it | 1.686 |
r_angle_refined_deg | 1.047 |
r_mcbond_it | 0.819 |
r_nbtor_refined | 0.307 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3096 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
HKL-2000 | data reduction |
SHELXD | phasing |