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Crystal structure of Menaquinol:fumarate oxidoreductase in complex with a 3-nitropropionate adduct
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.8 298 10% PEG 5000 mme, 250mM MgAc, 100mM Citrate pH 5.8, 0.1% w/v DTT, 0.1mM EDTA, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.97 69.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.065 α = 90 b = 139.006 β = 90 c = 276.476 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 ESRF BEAMLINE ID13 1.0 ESRF ID13
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 3.1 40 64420
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 3.1 40 64420 1181 93.5 0.255 0.255 0.254 0.279 0.2809 93.24
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] -0.1 -1.62 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.942 r_dihedral_angle_3_deg 16.247 r_dihedral_angle_4_deg 14.541 r_dihedral_angle_1_deg 4.752 r_angle_refined_deg 1.651 r_scangle_it 0.68 r_scbond_it 0.388 r_mcangle_it 0.261 r_mcbond_it 0.133 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.942 r_dihedral_angle_3_deg 16.247 r_dihedral_angle_4_deg 14.541 r_dihedral_angle_1_deg 4.752 r_angle_refined_deg 1.651 r_scangle_it 0.68 r_scbond_it 0.388 r_mcangle_it 0.261 r_mcbond_it 0.133 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 150
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction