3R6U

Crystal structure of choline binding protein OpuBC from Bacillus subtilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SW2PDB ENTRY 1SW2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.728520% PEG 3350, 0.2M potassium acetate, pH 8.7, VAPOR DIFFUSION, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
238.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.9α = 90
b = 66.9β = 93.6
c = 64.1γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.62093.5327933068522

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1SW21.6118.692327933007715831000.162630.160090.21016RANDOM15.022
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.608
r_dihedral_angle_4_deg15.678
r_dihedral_angle_3_deg14.594
r_dihedral_angle_1_deg5.958
r_scangle_it5.161
r_scbond_it3.26
r_angle_refined_deg2.092
r_mcangle_it2.008
r_mcbond_it1.281
r_chiral_restr0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.608
r_dihedral_angle_4_deg15.678
r_dihedral_angle_3_deg14.594
r_dihedral_angle_1_deg5.958
r_scangle_it5.161
r_scbond_it3.26
r_angle_refined_deg2.092
r_mcangle_it2.008
r_mcbond_it1.281
r_chiral_restr0.15
r_bond_refined_d0.027
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2175
Nucleic Acid Atoms
Solvent Atoms442
Heterogen Atoms7

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling