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Crystal structure of L-malate and NAD bound MDH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 288 0.1 M Na2HPO4:citric acid, 40% (v/v) polyethylene glycol 300, 10% DMSO
Crystal Properties Matthews coefficient Solvent content 2.47 50.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.982 α = 90 b = 152.14 β = 90 c = 155.035 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 CCD ADSC QUANTUM 270 2014-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 2.14 30.79 99.8 55.5 13.6 74182
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.14 30.79 74182 3924 98.45 0.21757 0.21612 0.2224 0.2442 0.2483 RANDOM 35.076
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 33.33 r_dihedral_angle_3_deg 13.157 r_dihedral_angle_4_deg 11.944 r_dihedral_angle_1_deg 5.133 r_long_range_B_refined 2.937 r_long_range_B_other 2.922 r_scangle_other 1.703 r_mcangle_it 1.461 r_mcangle_other 1.461 r_scbond_it 0.998
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.33 r_dihedral_angle_3_deg 13.157 r_dihedral_angle_4_deg 11.944 r_dihedral_angle_1_deg 5.133 r_long_range_B_refined 2.937 r_long_range_B_other 2.922 r_scangle_other 1.703 r_mcangle_it 1.461 r_mcangle_other 1.461 r_scbond_it 0.998 r_scbond_other 0.998 r_angle_refined_deg 0.984 r_mcbond_it 0.87 r_mcbond_other 0.87 r_angle_other_deg 0.76 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 102 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement