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Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with SH-1-96
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W84 PDB ENTRY 3W84
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 277 0.1M Cacodylate, 13% PEG3350, 0.05M Hexaamminecobalt (III) Chloride, 1mM Oxonate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.893 α = 90 b = 71.508 β = 90 c = 129.586 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 77 CCD ADSC QUANTUM 210 2013-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 50 89 0.057 9.7 5.7 90511 -3
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 1.53 83 0.409 3.95 5.4 4172
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 (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 3W84 1.5 31.64 88972 4454 87.24 0.1446 0.1426 0.1453 0.1838 0.1854 RANDOM 17.8057
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.536 r_dihedral_angle_4_deg 19.604 r_dihedral_angle_3_deg 12.762 r_dihedral_angle_1_deg 6.83 r_angle_refined_deg 2.422 r_angle_other_deg 1.11 r_chiral_restr 0.145 r_bond_refined_d 0.025 r_gen_planes_refined 0.016 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.536 r_dihedral_angle_4_deg 19.604 r_dihedral_angle_3_deg 12.762 r_dihedral_angle_1_deg 6.83 r_angle_refined_deg 2.422 r_angle_other_deg 1.11 r_chiral_restr 0.145 r_bond_refined_d 0.025 r_gen_planes_refined 0.016 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4776 Nucleic Acid Atoms Solvent Atoms 811 Heterogen Atoms 328
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection