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Crystal structure of Malate dehydrogenase from Metallosphaera sedula
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PLH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 35 %(v/v) 2-ethoxyethanol, 0.1M sodium cacodylate / hydrochloric acid pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.36 63.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.9 α = 90 b = 87.9 β = 90 c = 231.146 γ = 90
Symmetry Space Group P 43 21 2
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 2017-02-28 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 2.3 50 97.7 0.075 0.078 0.02 15.3 11.3 40297
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 2.3 2.34 95.1 0.271 0.296 0.114 0.858 5.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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 4PLH 2.3 50 38270 2006 97.78 0.1869 0.1841 0.1931 0.2423 0.243 RANDOM 53.705
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.637 r_dihedral_angle_4_deg 19.217 r_dihedral_angle_3_deg 17.879 r_dihedral_angle_1_deg 7.23 r_angle_refined_deg 1.941 r_angle_other_deg 1.076 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.637 r_dihedral_angle_4_deg 19.217 r_dihedral_angle_3_deg 17.879 r_dihedral_angle_1_deg 7.23 r_angle_refined_deg 1.941 r_angle_other_deg 1.076 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4630 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 100
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing HKL-2000 data reduction