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Plasmodium falciparum lactate dehydrogenase complexed with NAD+ and 4-hydroxy-1,2,5-oxadiazole-3-carboxylic acid
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 2.2 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.488 α = 90 b = 85.914 β = 90 c = 90.447 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 IMAGE PLATE MACSCIENCE mirrors 2000-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
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 1.7 29.36 100 0.058 18 2.7 34939 33448 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 1.7 1.76 100 0.188 5.1
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 1.7 29.36 33448 31423 1677 95 0.1437 0.1437 0.14247 0.146 0.16668 RANDOM 8.947
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] -0.41 0.98 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.351 r_dihedral_angle_1_deg 3.896 r_scangle_it 3.517 r_scbond_it 2.119 r_angle_refined_deg 1.544 r_angle_other_deg 1.206 r_mcangle_it 1.136 r_mcbond_it 0.586 r_symmetry_hbond_refined 0.448 r_nbtor_other 0.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.351 r_dihedral_angle_1_deg 3.896 r_scangle_it 3.517 r_scbond_it 2.119 r_angle_refined_deg 1.544 r_angle_other_deg 1.206 r_mcangle_it 1.136 r_mcbond_it 0.586 r_symmetry_hbond_refined 0.448 r_nbtor_other 0.446 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.213 r_nbd_other 0.194 r_symmetry_vdw_other 0.189 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2383 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing