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Crystal structure of the lactate dehydrogenase from cryptosporidium parvum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EWD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 16.5% PEG 2000, 0.1 M TRIS-HCL, 0.08% B-D-GLYCOPYRANOSIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.38 63.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.49 α = 90 b = 136.49 β = 90 c = 170.22 γ = 120
Symmetry Space Group P 32 1 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 MARRESEARCH 2005-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9998 APS 22-ID
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 2.1 20 94.9 0.062 15.8 3.8 100051
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 2.1 2.17 64.6 0.294 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2EWD 2.1 19.88 91538 4880 91.33 0.23157 0.23157 0.23031 0.224 0.25537 0.2477 RANDOM 53.287
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] 1.37 1.37 1.37 -4.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.918 r_dihedral_angle_4_deg 14.519 r_dihedral_angle_3_deg 11.179 r_dihedral_angle_1_deg 4.607 r_angle_refined_deg 0.844 r_angle_other_deg 0.65 r_chiral_restr 0.048 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.918 r_dihedral_angle_4_deg 14.519 r_dihedral_angle_3_deg 11.179 r_dihedral_angle_1_deg 4.607 r_angle_refined_deg 0.844 r_angle_other_deg 0.65 r_chiral_restr 0.048 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8905 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing