2I5M
Crystal structure of Bacillus subtilis cold shock protein CspB variant A46K S48R
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1CSP | pdb entry 1CSP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293.15 | reservoir solution: 1.5 M lithium sulfate, 0.1 M TRIS pH 7.5, 15% glycerol for cryoprotection. protein solution: 20 mM TRIS pH 7.5, 50 mM NaCl, 3 mM MgCl2, 17.4 mg/ml protein. crystallization setup: 0.8 microliter protein solution:0.8 microliter reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.09 | 60.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.627 | α = 90 |
b = 58.627 | β = 90 |
c = 46.798 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | 110 | CCD | MAR CCD 165 mm | mirrors | 2005-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.9537 | BESSY | 14.2 |
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 | 2.22 | 20 | 98.319 | 0.049 | 26.65 | 6.7 | 4700 | 4621 | 41.593 |
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 | 2.22 | 2.3 | 83.3 | 0.157 | 7.9 | 5.4 | 390 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 1CSP | 2.3 | 19.19 | 4290 | 4231 | 214 | 98.624 | 0.205 | 0.204 | 0.227 | RANDOM | 33.462 |
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] | |
2.08 | 1.04 | 2.08 | -3.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.867 |
r_scangle_it | 2.386 |
r_angle_other_deg | 2.018 |
r_angle_refined_deg | 1.617 |
r_scbond_it | 1.483 |
r_mcangle_it | 1.066 |
r_mcbond_it | 0.582 |
r_symmetry_vdw_other | 0.275 |
r_nbd_other | 0.187 |
r_symmetry_hbond_refined | 0.179 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 521 |
Nucleic Acid Atoms | |
Solvent Atoms | 23 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
AMoRE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
XDS | data reduction |