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Plasmodium falciparum lactate dehydrogenase S245A, A327P mutant complexed with NADH and oxamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.066 α = 90 b = 85.336 β = 90 c = 89.714 γ = 90
Symmetry Space Group I 2 2 2
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 4 2001-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
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 1.85 20 98.8 0.059 21.3 4.9 26293 25934 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.93 96.2 0.289 3.7 3153
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1LDG 1.85 20 24726 23475 1251 94.02 0.15761 0.15761 0.1558 0.1586 0.19076 RANDOM 17.181
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] -1.06 1.28 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.33 r_scangle_it 5.473 r_dihedral_angle_1_deg 4.249 r_scbond_it 3.371 r_angle_refined_deg 2.375 r_mcangle_it 1.938 r_mcbond_it 1.157 r_symmetry_hbond_refined 0.942 r_nbd_refined 0.358 r_symmetry_vdw_refined 0.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.33 r_scangle_it 5.473 r_dihedral_angle_1_deg 4.249 r_scbond_it 3.371 r_angle_refined_deg 2.375 r_mcangle_it 1.938 r_mcbond_it 1.157 r_symmetry_hbond_refined 0.942 r_nbd_refined 0.358 r_symmetry_vdw_refined 0.287 r_chiral_restr 0.174 r_xyhbond_nbd_refined 0.159 r_bond_refined_d 0.023 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2404 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing