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Crystal structure of a putative Cytosolic malate dehydrogenase from Leishmania major Friedlin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IZ9 PDB entry 1IZ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 EmeraldBio JCSG+ screen h7: 25% PEG 3350, 200mM ammonium sulphate, 100mM BisTris pH 5.5; LemaA.01212.a.A1.P001468 at 20mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.58 α = 90 b = 65.66 β = 110.11 c = 77.65 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 QUANTUM 315r 2012-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
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 1.3 50 97.9 0.047 0.047 24.71 9.7 146529 -3 21.987
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 1.3 1.33 94 0.336 4.11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT PDB entry 1IZ9 1.3 28.92 149715 146506 7367 97.95 0.1534 0.1534 0.1522 0.1521 0.1785 0.1783 RANDOM 21.4934
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] 0.48 0.57 -0.1 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.581 r_dihedral_angle_4_deg 15.204 r_dihedral_angle_3_deg 11.217 r_dihedral_angle_1_deg 6.372 r_angle_refined_deg 1.656 r_angle_other_deg 0.847 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.581 r_dihedral_angle_4_deg 15.204 r_dihedral_angle_3_deg 11.217 r_dihedral_angle_1_deg 6.372 r_angle_refined_deg 1.656 r_angle_other_deg 0.847 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4438 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 25
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction