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Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES (pH 7.5), 10 % polyethylene glycol (PEG) 6000, 5 % 2-Methyl-2,4-pentanediol (MPD)
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.682 α = 90 b = 108.679 β = 90 c = 146.643 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 PILATUS3 6M 2018-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 1.945 50 99.7 0.079 0.998 11.2 11.8 95978
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 1.95 1.98 0.596 0.835
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 3TL2 1.945 44.619 95909 4804 99.501 0.208 0.2059 0.211 0.2546 0.2536 39.396
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 0.011 -0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.414 r_dihedral_angle_3_deg 16.167 r_dihedral_angle_4_deg 11.469 r_dihedral_angle_1_deg 7.007 r_lrange_other 6.356 r_lrange_it 6.35 r_scangle_other 5.282 r_scangle_it 5.281 r_mcangle_it 4.059 r_mcangle_other 4.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.414 r_dihedral_angle_3_deg 16.167 r_dihedral_angle_4_deg 11.469 r_dihedral_angle_1_deg 7.007 r_lrange_other 6.356 r_lrange_it 6.35 r_scangle_other 5.282 r_scangle_it 5.281 r_mcangle_it 4.059 r_mcangle_other 4.059 r_scbond_it 3.535 r_scbond_other 3.533 r_mcbond_it 3.124 r_mcbond_other 3.124 r_angle_refined_deg 1.515 r_angle_other_deg 1.282 r_nbd_other 0.233 r_nbd_refined 0.195 r_symmetry_nbd_other 0.176 r_symmetry_nbd_refined 0.165 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9290 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing