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Crystal structure of malate dehydrogenase from Porphyromonas gingivalis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 294 20% PEG 3350, 200mM ammonium di-tartrate, pH 7.0, vapor diffusion, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.4 48.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.385 α = 90 b = 74.133 β = 90 c = 135.296 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 CCD MAR CCD 165 mm 2008-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 40.937 99.3 0.112 0.112 9 7 57291 56890 19
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 1.9 2 98 0.378 0.378 3.2 6.8 8079
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.9 20 57283 56773 2847 99.11 0.254 0.252 0.2424 0.295 0.2804 RANDOM 23.562
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] -1.71 4.05 -2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.522 r_dihedral_angle_4_deg 15.626 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_1_deg 5.499 r_scangle_it 4.384 r_scbond_it 2.877 r_mcangle_it 1.525 r_angle_refined_deg 1.467 r_mcbond_it 0.864 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.522 r_dihedral_angle_4_deg 15.626 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_1_deg 5.499 r_scangle_it 4.384 r_scbond_it 2.877 r_mcangle_it 1.525 r_angle_refined_deg 1.467 r_mcbond_it 0.864 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4798 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXCD phasing SHELXE model building