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Plasmodium falciparum lactate dehydrogenase complexed with 2,6-naphthalenedicarboxylic acid
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 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.196 α = 90 b = 85.225 β = 90 c = 92.232 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 MAC Science DIP-2020 Mirrors 2001-09-03 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 30 96 0.087 13.5 7 33794 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 1.78 93.2 0.29 3.3 3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1LDG 1.7 29.24 33274 31601 1673 94.57 0.14689 0.14689 0.14514 0.18054 0.1928 RANDOM 11.329
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] -0.44 1.03 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.555 r_scangle_it 3.137 r_scbond_it 1.969 r_angle_refined_deg 1.39 r_angle_other_deg 1.354 r_mcangle_it 1.145 r_mcbond_it 0.654 r_nbd_refined 0.321 r_symmetry_vdw_other 0.268 r_nbd_other 0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.555 r_scangle_it 3.137 r_scbond_it 1.969 r_angle_refined_deg 1.39 r_angle_other_deg 1.354 r_mcangle_it 1.145 r_mcbond_it 0.654 r_nbd_refined 0.321 r_symmetry_vdw_other 0.268 r_nbd_other 0.235 r_symmetry_hbond_refined 0.181 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.112 r_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_other 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2342 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing