2I5M

Crystal structure of Bacillus subtilis cold shock protein CspB variant A46K S48R


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.15reservoir 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
Matthews coefficientSolvent content
3.0960.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.627α = 90
b = 58.627β = 90
c = 46.798γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMAR CCD 165 mmmirrors2005-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9537BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.222098.3190.04926.656.74700462141.593
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.222.383.30.1577.95.4390

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1CSP2.319.194290423121498.6240.2050.2040.227RANDOM33.462
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]
2.081.042.08-3.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.867
r_scangle_it2.386
r_angle_other_deg2.018
r_angle_refined_deg1.617
r_scbond_it1.483
r_mcangle_it1.066
r_mcbond_it0.582
r_symmetry_vdw_other0.275
r_nbd_other0.187
r_symmetry_hbond_refined0.179
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.867
r_scangle_it2.386
r_angle_other_deg2.018
r_angle_refined_deg1.617
r_scbond_it1.483
r_mcangle_it1.066
r_mcbond_it0.582
r_symmetry_vdw_other0.275
r_nbd_other0.187
r_symmetry_hbond_refined0.179
r_nbd_refined0.158
r_xyhbond_nbd_refined0.158
r_nbtor_other0.083
r_chiral_restr0.075
r_symmetry_vdw_refined0.061
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms521
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms1

Software

Software
Software NamePurpose
XSCALEdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction