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Plasmodium falciparum lactate dehydrogenase complexed with 3,7-dihydroxynaphthalene-2-carboxylic acid and NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDG PDB entry 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 2.36 47.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.225 α = 90 b = 86.017 β = 90 c = 91.07 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 2001-09-14 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 2.6 30 97.6 0.127 7.1 7 10105 9848 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 2.6 2.69 99 0.294 3.1 3 992
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 1LDG 2.65 29.36 9013 8572 441 95.28 0.1579 0.1579 0.15374 0.1642 0.23945 0.2395 RANDOM 14.362
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] -1.52 1.65 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.201 r_scangle_it 2.941 r_scbond_it 1.721 r_angle_refined_deg 1.587 r_mcangle_it 1.217 r_angle_other_deg 0.793 r_mcbond_it 0.653 r_nbd_refined 0.312 r_symmetry_vdw_other 0.277 r_nbd_other 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.201 r_scangle_it 2.941 r_scbond_it 1.721 r_angle_refined_deg 1.587 r_mcangle_it 1.217 r_angle_other_deg 0.793 r_mcbond_it 0.653 r_nbd_refined 0.312 r_symmetry_vdw_other 0.277 r_nbd_other 0.237 r_symmetry_hbond_refined 0.22 r_xyhbond_nbd_refined 0.186 r_symmetry_vdw_refined 0.181 r_nbtor_other 0.087 r_chiral_restr 0.075 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2305 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing