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Crystal structure of malate dehydrogenase from Plasmodium Falciparum in complex with 4-(3,4-difluorophenyl)thiazol-2-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.4 M trisodium citrate, 0.1 M Hepes
Crystal Properties Matthews coefficient Solvent content 2.32 47.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.76 α = 90 b = 106.89 β = 90 c = 145.01 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 PIXEL Bruker PHOTON II 2019-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.540
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 50 99.9 0.2 21.1 14.1 89246
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.12
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 5nfr 2 48.97 84786 4463 99.87 0.21167 0.21025 0.2171 0.23846 0.2425 RANDOM 33.266
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] -0.06 0.31 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.417 r_dihedral_angle_3_deg 15.059 r_dihedral_angle_4_deg 12.512 r_long_range_B_refined 11.371 r_long_range_B_other 11.364 r_dihedral_angle_1_deg 7.516 r_scangle_other 3.782 r_mcangle_it 3.05 r_mcangle_other 3.05 r_scbond_it 2.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.417 r_dihedral_angle_3_deg 15.059 r_dihedral_angle_4_deg 12.512 r_long_range_B_refined 11.371 r_long_range_B_other 11.364 r_dihedral_angle_1_deg 7.516 r_scangle_other 3.782 r_mcangle_it 3.05 r_mcangle_other 3.05 r_scbond_it 2.396 r_scbond_other 2.396 r_angle_other_deg 2.358 r_mcbond_it 1.95 r_mcbond_other 1.95 r_angle_refined_deg 1.885 r_chiral_restr 0.09 r_bond_other_d 0.036 r_bond_refined_d 0.015 r_gen_planes_other 0.014 r_gen_planes_refined 0.009 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 9482 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing