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Crystal structure of Malate dehydrogenase from Metallosphaera sedula
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 293 40 % (v/v) polyethylene glycol (PEG) 300, 0.1 M CHES / sodium hydroxide pH 9.5, 0.2 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 3.21 61.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.194 α = 90 b = 134.194 β = 90 c = 81.94 γ = 120
Symmetry Space Group P 31 2 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 CCD ADSC QUANTUM 270 2017-12-17 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 96.7 0.071 0.076 0.025 11.9 6.8 65061
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 97.4 0.333 0.373 0.162 0.754 4.4
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 MOLECULAR REPLACEMENT THROUGHOUT 1.9 50 61878 3181 96.59 0.1938 0.1922 0.2024 0.2258 0.2303 RANDOM 36.481
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 40.333 r_dihedral_angle_3_deg 14.933 r_dihedral_angle_4_deg 14.009 r_dihedral_angle_1_deg 6.581 r_angle_refined_deg 1.977 r_angle_other_deg 1.067 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.333 r_dihedral_angle_3_deg 14.933 r_dihedral_angle_4_deg 14.009 r_dihedral_angle_1_deg 6.581 r_angle_refined_deg 1.977 r_angle_other_deg 1.067 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4652 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction MOLREP phasing