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Plasmodium falciparum lactate dehydrogenase complexed with 2,6-naphthalenedisulphonic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDG PDB model 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 2.4 48.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.094 α = 90 b = 86.096 β = 90 c = 91.327 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 30 90.9 0.055 13.6 6 19866 19866 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 2.15 79.5 0.174 4.1 2 3421
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 model 1LDG 2 29.36 20360 19321 1039 94.25 0.13843 0.13843 0.13578 0.1503 0.18767 0.1995 RANDOM 16.842
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] -1.6 1.73 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.685 r_scangle_it 3.76 r_scbond_it 2.325 r_angle_refined_deg 1.481 r_mcangle_it 1.336 r_angle_other_deg 0.829 r_mcbond_it 0.77 r_nbd_refined 0.316 r_symmetry_vdw_other 0.291 r_nbd_other 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.685 r_scangle_it 3.76 r_scbond_it 2.325 r_angle_refined_deg 1.481 r_mcangle_it 1.336 r_angle_other_deg 0.829 r_mcbond_it 0.77 r_nbd_refined 0.316 r_symmetry_vdw_other 0.291 r_nbd_other 0.24 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.088 r_nbtor_other 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2322 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing