☰ Navigation Tabs
Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Nicotinamide Adenine Dinucleotide (NAD)
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 The crystal of wild-type gs-MDH prepared in 0.1 M HEPES (pH 7.5), 10 % polyethylene glycol (PEG) 6000 and 5 % 2-Methyl-2,4-pentanediol (MPD) was soaked into the cryo-protectant containing 2 mM OAA and 2 mM NAD+.
Crystal Properties Matthews coefficient Solvent content 2.32 47.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.156 α = 90 b = 83.239 β = 93.42 c = 119.477 γ = 90
Symmetry Space Group P 1 21 1
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 2018-10-14 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 50 99 0.198 0.966 4 4.6 62899
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 2.26 0.535 0.913 1.6
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 39.393 62624 3047 99.564 0.226 0.2235 0.2334 0.2848 0.2878 42.666
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] -0.024 -0.034 0.034 -0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.676 r_dihedral_angle_3_deg 20.495 r_dihedral_angle_4_deg 16.038 r_dihedral_angle_1_deg 7.925 r_lrange_it 7.314 r_lrange_other 7.313 r_mcangle_it 5.537 r_mcangle_other 5.537 r_scangle_it 5.073 r_scangle_other 5.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.676 r_dihedral_angle_3_deg 20.495 r_dihedral_angle_4_deg 16.038 r_dihedral_angle_1_deg 7.925 r_lrange_it 7.314 r_lrange_other 7.313 r_mcangle_it 5.537 r_mcangle_other 5.537 r_scangle_it 5.073 r_scangle_other 5.072 r_mcbond_it 4.203 r_mcbond_other 4.203 r_scbond_it 3.831 r_scbond_other 3.831 r_angle_refined_deg 1.694 r_angle_other_deg 1.188 r_symmetry_nbd_refined 0.273 r_nbd_other 0.234 r_xyhbond_nbd_refined 0.209 r_nbd_refined 0.206 r_symmetry_nbd_other 0.197 r_symmetry_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_other 0.106 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9332 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing