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Crystal structure of a putative Cytosolic malate dehydrogenase from Leishmania major Friedlin in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H7P PDB ENTRY 4H7P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 290 EmeraldBio PACT screen a3: 25% PEG 1500, 100mM SPG buffer pH 6.0; LemaA.01212.a.A1.P001468 at 15mg/ml + 2.5mM NAD, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.1 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.82 α = 90 b = 65.13 β = 110.67 c = 77.49 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 MARMOSAIC 225 mm CCD 2012-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.5 50 99.2 0.059 12.27 3.7 96750 95941 -3 25.149
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 1.5 1.54 94.2 0.35 0.35 2.78 2.6 7124
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 4H7P 1.5 48.5 96750 95920 4794 99.26 0.1459 0.1459 0.1449 0.1441 0.1655 0.1649 RANDOM 21.1806
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] 0.09 0.07 0.1 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.382 r_dihedral_angle_4_deg 14.204 r_dihedral_angle_3_deg 11.232 r_dihedral_angle_1_deg 6.367 r_mcangle_it 1.84 r_angle_refined_deg 1.664 r_mcbond_it 1.189 r_mcbond_other 1.189 r_angle_other_deg 0.803 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.382 r_dihedral_angle_4_deg 14.204 r_dihedral_angle_3_deg 11.232 r_dihedral_angle_1_deg 6.367 r_mcangle_it 1.84 r_angle_refined_deg 1.664 r_mcbond_it 1.189 r_mcbond_other 1.189 r_angle_other_deg 0.803 r_chiral_restr 0.102 r_bond_refined_d 0.015 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 4567 Nucleic Acid Atoms Solvent Atoms 623 Heterogen Atoms 79
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing