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WrbA from Escherichia coli, Benzoquinone complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B6I PDB entry 3B6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 15-35 % Polyethylene Glycol, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.67 73.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.239 α = 90 b = 94.239 β = 90 c = 175.554 γ = 90
Symmetry Space Group P 43 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 IMAGE PLATE MAR scanner 345 mm plate osmic mirrors 2007-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54180
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.95 50 99.5 0.11 6.2 5.9 59358 59061 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.05 97.3 0.58 1.8 5.2 59358
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 3B6I 1.99 36.7 2 2 59358 51052 2743 97.39 0.17367 0.17185 0.1726 0.20783 0.2074 RANDOM 32.403
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] 0.56 0.56 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.986 r_dihedral_angle_4_deg 16.661 r_dihedral_angle_3_deg 15.126 r_dihedral_angle_1_deg 6.06 r_scangle_it 3.981 r_scbond_it 2.531 r_angle_refined_deg 1.686 r_mcangle_it 1.46 r_mcbond_it 0.91 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.986 r_dihedral_angle_4_deg 16.661 r_dihedral_angle_3_deg 15.126 r_dihedral_angle_1_deg 6.06 r_scangle_it 3.981 r_scbond_it 2.531 r_angle_refined_deg 1.686 r_mcangle_it 1.46 r_mcbond_it 0.91 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.262 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.106 r_bond_refined_d 0.017 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2916 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing