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Reconstructed ancestral trichomonad malate dehydrogenase in complex with NADH, SO4, and PO4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MDH HOMOLOGY MODEL BASED ON PDB ENTRY 5MDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 5 MG/ML PROTEIN, 100 MM TRIS, PH 8.0, 25% PEG 4000, AND 0.2M LI2SO4
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.46 α = 90 b = 58.85 β = 111.23 c = 81.57 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 CCD ADSC CCD 2012-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.54 46.5 93.6 0.083 14.59 8.3 91959 0.65 22.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.58 58.6 1.331 1.11 0.65
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT HOMOLOGY MODEL BASED ON PDB ENTRY 5MDH 1.543 46.539 1.33 91936 4569 93.72 0.1684 0.1667 0.1707 0.2003 0.2048 34.1
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 f_dihedral_angle_d 12.368 f_angle_d 1.02 f_chiral_restr 0.054 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5053 Nucleic Acid Atoms Solvent Atoms 598 Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing