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Crystal structure of Menaquinol:oxidoreductase in complex with oxaloacetate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.8 298 12.5% PEG 5000 mme, 85mM MgAc, 100mM Citrate pH 5.8, 0.1% w/v DTT, 0.1mM EDTA, 5mM fumarate, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.84 67.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.641 α = 90 b = 137.964 β = 90 c = 272.803 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.0 SSRL BL9-2
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 3.35 50 88.9 0.099 10.2 3.1 47456
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) 3.35 3.47 73.9 0.237 2.2
Refinement Statistics Diffraction ID Structure Solution Method 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) Mean Isotropic B X-RAY DIFFRACTION 3.35 47.57 47428 920 89.2 0.221 0.22 0.2194 0.261 0.2573 95.455
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] -0.11 -3.1 3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.661 r_dihedral_angle_3_deg 17.4 r_dihedral_angle_4_deg 15.539 r_dihedral_angle_1_deg 4.973 r_angle_refined_deg 1.868 r_scangle_it 0.839 r_mcangle_it 0.518 r_scbond_it 0.468 r_chiral_restr 0.449 r_mcbond_it 0.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.661 r_dihedral_angle_3_deg 17.4 r_dihedral_angle_4_deg 15.539 r_dihedral_angle_1_deg 4.973 r_angle_refined_deg 1.868 r_scangle_it 0.839 r_mcangle_it 0.518 r_scbond_it 0.468 r_chiral_restr 0.449 r_mcbond_it 0.281 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16642 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 162
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction