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Crystal structure of ancestral apicomplexan malate dehydrogenase with lactate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20mg/mL protein with 2mM NADH/L-lactate; well solution: 20% (w/v) PEG-1500, 0.1M HEPES, pH7.5
Crystal Properties Matthews coefficient Solvent content 2.43 49.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.367 α = 90 b = 103.738 β = 90 c = 143.723 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 90 CCD ADSC QUANTUM 315r 2012-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.115866 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 1.85 50 99.9 0.148 12.47 8.1 115626 32.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.96 99.5 3.35 0.66 8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 FREE R-VALUE 2HJR 1.85 48.789 1.33 218309 3154 97.89 0.1828 0.1822 0.1837 0.2212 0.2234 36.9145
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 15.573 f_angle_d 1.012 f_chiral_restr 0.039 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9537 Nucleic Acid Atoms Solvent Atoms 1039 Heterogen Atoms 196
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection XDS data reduction PDB_EXTRACT data extraction