2HAX
Crystal structure of Bacillus caldolyticus cold shock protein in complex with hexathymidine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1C9O | PDB entry 1C9O |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 293.15 | 35% 2-methyl-2,4-pentanediol, 0.1 M sodium acetate pH 4.6, 0.02 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.34 | α = 90 |
b = 64.89 | β = 90 |
c = 31.2 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 110 | CCD | MAR CCD 165 mm | mirrors | 2003-10-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | BESSY | 14.1 |
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 | 1.29 | 19.5 | 97.9 | 0.066 | 14.68 | 6.3 | 38879 | 38068 | -3 | -3 | 16.166 |
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) | |||||||||||
1.29 | 1.5 | 95.1 | 0.239 | 6.1 | 6.2 | 13269 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1C9O | 1.29 | 19.5 | 38036 | 36128 | 1908 | 95 | 0.132 | 0.132 | 0.13 | 0.162 | RANDOM | 10.87 |
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] | |
-0.37 | -0.25 | 0.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 14.831 |
r_sphericity_bonded | 6.33 |
r_scangle_it | 5.166 |
r_dihedral_angle_1_deg | 4.346 |
r_scbond_it | 3.878 |
r_mcangle_it | 3.158 |
r_mcbond_it | 2.177 |
r_angle_refined_deg | 1.567 |
r_rigid_bond_restr | 1.479 |
r_angle_other_deg | 0.98 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1117 |
Nucleic Acid Atoms | 246 |
Solvent Atoms | 250 |
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 scaling |