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Crystal structure of Plasmodium vivax lactate dehydrogenase complex with APADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A92 PDB Entry 2A92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 PEG5k MME, Ammonium sulphate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.37 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.482 α = 90 b = 128.454 β = 90 c = 130.781 γ = 90
Symmetry Space Group P 21 21 21
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 2005-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
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 2.05 91.67 98.4 0.099 21.3 8.2 85499 85499 2 27.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.05 2.12 96.9 96.9 0.379 0.379 4.6 7.8
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 2A92 2.05 91.67 85499 85445 4276 98.33 0.192 0.192 0.191 0.1914 0.226 0.2249 RANDOM 20.838
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] -0.16 -0.45 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.455 r_dihedral_angle_3_deg 14.906 r_dihedral_angle_4_deg 14.822 r_dihedral_angle_1_deg 6.528 r_scangle_it 3.333 r_scbond_it 2.4 r_angle_refined_deg 1.783 r_mcangle_it 1.457 r_mcbond_it 0.95 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.455 r_dihedral_angle_3_deg 14.906 r_dihedral_angle_4_deg 14.822 r_dihedral_angle_1_deg 6.528 r_scangle_it 3.333 r_scbond_it 2.4 r_angle_refined_deg 1.783 r_mcangle_it 1.457 r_mcbond_it 0.95 r_nbtor_refined 0.302 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.126 r_symmetry_hbond_refined 0.122 r_bond_refined_d 0.022 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9637 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 186
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction