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Structure of Plasmodium falciparum lactate dehydrogenase complexed to APADH.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T2C PDB Entry 1T2C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.31 46.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.183 α = 90 b = 86.208 β = 90 c = 90.826 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 2001-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.978 SRS PX14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.5 30 99.5 0.031 37.4 4.5 51103 50501 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.62 99.5 99.5 0.133 7.3 4.1
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 1T2C 1.5 29.36 50719 48267 2452 95.28 0.16 0.16 0.16 0.161 0.176 0.176 RANDOM 10.543
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] -0.9 1.08 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.579 r_dihedral_angle_1_deg 4.068 r_scangle_it 3.741 r_scbond_it 2.26 r_angle_other_deg 1.543 r_angle_refined_deg 1.533 r_mcangle_it 1.362 r_mcbond_it 0.714 r_nbtor_other 0.582 r_symmetry_hbond_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.579 r_dihedral_angle_1_deg 4.068 r_scangle_it 3.741 r_scbond_it 2.26 r_angle_other_deg 1.543 r_angle_refined_deg 1.533 r_mcangle_it 1.362 r_mcbond_it 0.714 r_nbtor_other 0.582 r_symmetry_hbond_refined 0.332 r_nbd_refined 0.225 r_symmetry_vdw_other 0.207 r_symmetry_vdw_refined 0.198 r_nbd_other 0.19 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.091 r_bond_refined_d 0.012 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 214 Heterogen Atoms 44
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction AMoRE phasing