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Crystal structure of choline binding protein OpuBC from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SW2 PDB ENTRY 1SW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.7 285 20% PEG 3350, 0.2M potassium acetate, pH 8.7, VAPOR DIFFUSION, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2 38.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.9 α = 90 b = 66.9 β = 93.6 c = 64.1 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2010-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 20 93.5 32793 30685 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SW2 1.61 18.69 2 32793 30077 1583 100 0.16263 0.16009 0.1601 0.21016 0.2082 RANDOM 15.022
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.608 r_dihedral_angle_4_deg 15.678 r_dihedral_angle_3_deg 14.594 r_dihedral_angle_1_deg 5.958 r_scangle_it 5.161 r_scbond_it 3.26 r_angle_refined_deg 2.092 r_mcangle_it 2.008 r_mcbond_it 1.281 r_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.608 r_dihedral_angle_4_deg 15.678 r_dihedral_angle_3_deg 14.594 r_dihedral_angle_1_deg 5.958 r_scangle_it 5.161 r_scbond_it 3.26 r_angle_refined_deg 2.092 r_mcangle_it 2.008 r_mcbond_it 1.281 r_chiral_restr 0.15 r_bond_refined_d 0.027 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2175 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 7
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling