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Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Adenosine 5'-Diphosphoribose (APR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Tris-HCl (pH 7.0), 16 % PEG 2000 MME, 2 mM OAA, and 2 mM NAD+
Crystal Properties Matthews coefficient Solvent content 2.4 48.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.327 α = 90 b = 103.22 β = 90 c = 150.79 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 PIXEL DECTRIS EIGER X 4M 2019-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.2 49.16 100 0.111 0.999 21.8 27.6 66776
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.25 0.441 0.99 8.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7BY8 2.2 49.159 66701 3434 99.988 0.183 0.1804 0.1897 0.2299 0.2326 48.842
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] 0.002 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.936 r_dihedral_angle_3_deg 15.875 r_dihedral_angle_4_deg 15.535 r_lrange_other 6.924 r_lrange_it 6.923 r_dihedral_angle_1_deg 6.886 r_scangle_it 5.857 r_scangle_other 5.856 r_mcangle_it 4.542 r_mcangle_other 4.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.936 r_dihedral_angle_3_deg 15.875 r_dihedral_angle_4_deg 15.535 r_lrange_other 6.924 r_lrange_it 6.923 r_dihedral_angle_1_deg 6.886 r_scangle_it 5.857 r_scangle_other 5.856 r_mcangle_it 4.542 r_mcangle_other 4.542 r_scbond_it 4.078 r_scbond_other 4.076 r_mcbond_it 3.536 r_mcbond_other 3.534 r_angle_refined_deg 1.469 r_angle_other_deg 1.266 r_symmetry_xyhbond_nbd_refined 0.316 r_nbd_refined 0.196 r_nbd_other 0.183 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.154 r_xyhbond_nbd_refined 0.135 r_symmetry_nbd_refined 0.077 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9375 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing