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Crystal structure of citrate bound MDH2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DFD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 288 0.1M Na2HPO4, citric acid, 40% (v/v) polyethylene glycol 300
Crystal Properties Matthews coefficient Solvent content 2.43 49.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.695 α = 90 b = 151.22 β = 90 c = 154.645 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 100 IMAGE PLATE MAR scanner 300 mm plate 2014-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
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 1.9 45.1 99.8 31.3 7.1 104532
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 2DFD 1.9 45.1 104532 5506 99.53 0.2194 0.2184 0.2236 0.23806 0.2435 RANDOM 35.047
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] 0.03 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.498 r_dihedral_angle_3_deg 12.578 r_dihedral_angle_4_deg 11.321 r_dihedral_angle_1_deg 4.863 r_long_range_B_refined 2.536 r_long_range_B_other 2.531 r_scangle_other 1.62 r_mcangle_it 1.389 r_mcangle_other 1.389 r_scbond_it 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.498 r_dihedral_angle_3_deg 12.578 r_dihedral_angle_4_deg 11.321 r_dihedral_angle_1_deg 4.863 r_long_range_B_refined 2.536 r_long_range_B_other 2.531 r_scangle_other 1.62 r_mcangle_it 1.389 r_mcangle_other 1.389 r_scbond_it 0.95 r_scbond_other 0.949 r_angle_refined_deg 0.898 r_mcbond_it 0.819 r_mcbond_other 0.819 r_angle_other_deg 0.68 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9248 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement