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Crystal structure of malate dehydrogenase from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V9N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 JCSG+ sparse matrix screen condition a2, 20% PEG 3000, 0.1 M Na Citrate pH 5.5, 25% glycerol as cryo-protectant, 30 mg/mL protein, crystal ID 203003a2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.9 57.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.23 α = 90 b = 106.23 β = 90 c = 72.114 γ = 120
Symmetry Space Group P 3 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 2009-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 2.6 38.78 99.1 0.144 13.75 7.5 14659
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 2.6 2.69 94.7 0.536 2.18 5.4 1371
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1v9n 2.6 38.78 14657 732 99.07 0.184 0.182 0.232 0.1695 RANDOM 27.582
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] 1.4 0.7 1.4 -2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.889 r_dihedral_angle_4_deg 17.748 r_dihedral_angle_3_deg 16.305 r_dihedral_angle_1_deg 5.522 r_scangle_it 2.079 r_angle_refined_deg 1.208 r_scbond_it 1.193 r_mcangle_it 0.832 r_mcbond_it 0.427 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.889 r_dihedral_angle_4_deg 17.748 r_dihedral_angle_3_deg 16.305 r_dihedral_angle_1_deg 5.522 r_scangle_it 2.079 r_angle_refined_deg 1.208 r_scbond_it 1.193 r_mcangle_it 0.832 r_mcbond_it 0.427 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2793 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 50
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling