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Crystal structure of malate dehydrogenase from Plasmodium falciparum (PfMDH)
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, SITTING DROP 7.22 293 100 mM Ammonium citrate pH 7.22
22% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.93 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.018 α = 103.77 b = 152.689 β = 101.46 c = 158.393 γ = 94.93
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 2012-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97841 ESRF BM14
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 2.24 47.62 89.5 0.053 10.46 2.12 273174
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 2.24 2.38 64.3 0.456 1.57
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2HJR 2.4 47.6 230493 12225 97.62 0.2489 0.24809 0.2691 0.26423 0.2812 RANDOM 23.491
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] -0.15 -0.65 -0.66 -3.39 0.19 3.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.661 r_dihedral_angle_4_deg 20.776 r_dihedral_angle_3_deg 15.704 r_dihedral_angle_1_deg 6.005 r_long_range_B_refined 4.82 r_long_range_B_other 4.82 r_scangle_other 3.188 r_mcangle_it 2.821 r_mcangle_other 2.821 r_scbond_it 1.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.661 r_dihedral_angle_4_deg 20.776 r_dihedral_angle_3_deg 15.704 r_dihedral_angle_1_deg 6.005 r_long_range_B_refined 4.82 r_long_range_B_other 4.82 r_scangle_other 3.188 r_mcangle_it 2.821 r_mcangle_other 2.821 r_scbond_it 1.925 r_scbond_other 1.925 r_angle_refined_deg 1.734 r_mcbond_it 1.671 r_mcbond_other 1.671 r_angle_other_deg 1.635 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_bond_other_d 0.014 r_gen_planes_refined 0.014 r_gen_planes_other 0.012 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 38114 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 195
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing