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Crystal structure of lactate dehydrogenase from Plasmodium vivax: complex with NADH
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 6.1 291 PEG 5000 monoethylether, Ammonium Sulphate, Mes, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.39 48.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.593 α = 90 b = 128.636 β = 90 c = 130.58 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 2004-11-24 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 91.29 98.2 0.108 11.8 3.9 98204 98204 2 26.95
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 2 2.1 97.5 97.3 0.434 2.4 3.8 9639
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 2.04 91.29 90148 85849 4299 97.82 0.197 0.197 0.194 0.1923 0.236 0.232 RANDOM 9.716
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] 1.44 -1.85 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.529 r_dihedral_angle_3_deg 14.824 r_dihedral_angle_4_deg 14.051 r_dihedral_angle_1_deg 7.112 r_scangle_it 2.752 r_scbond_it 1.9 r_angle_refined_deg 1.525 r_mcangle_it 1.08 r_mcbond_it 0.721 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.529 r_dihedral_angle_3_deg 14.824 r_dihedral_angle_4_deg 14.051 r_dihedral_angle_1_deg 7.112 r_scangle_it 2.752 r_scbond_it 1.9 r_angle_refined_deg 1.525 r_mcangle_it 1.08 r_mcbond_it 0.721 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9596 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 176
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction AMoRE phasing