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Crystal structure of E. coli WrbA in complex with benzoquinone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 0.1 M MES/Imidazol, 12.5 % PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.2M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol,
0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol
Crystal Properties Matthews coefficient Solvent content 1.92 35.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.179 α = 90 b = 61.179 β = 90 c = 169.992 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall 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 1.33 42.5 99.9 0.049 18.02 5.63 142025 141939 20.75
Highest Resolution Shell 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 1.33 1.41 99.8 0.657 2.36
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2RG1 1.33 42.5 71491 3763 99.92 0.1266 0.1248 0.1255 0.1608 0.1612 RANDOM 21.479
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.375 r_sphericity_free 28.296 r_dihedral_angle_4_deg 12.897 r_sphericity_bonded 11.336 r_dihedral_angle_3_deg 10.971 r_dihedral_angle_1_deg 5.576 r_rigid_bond_restr 3.235 r_mcangle_it 2.998 r_mcbond_it 2.511 r_mcbond_other 2.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.375 r_sphericity_free 28.296 r_dihedral_angle_4_deg 12.897 r_sphericity_bonded 11.336 r_dihedral_angle_3_deg 10.971 r_dihedral_angle_1_deg 5.576 r_rigid_bond_restr 3.235 r_mcangle_it 2.998 r_mcbond_it 2.511 r_mcbond_other 2.502 r_angle_refined_deg 1.642 r_angle_other_deg 1.117 r_chiral_restr 0.094 r_gen_planes_refined 0.015 r_bond_refined_d 0.013 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2806 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement MOLREP phasing PDB_EXTRACT data extraction XDS data reduction Coot model building XSCALE data scaling