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Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-013
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W71 PDB ENTRY 3W71
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 46.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.95 α = 90 b = 71.828 β = 90 c = 129.239 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 315 2009-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.55 50 93.1 0.058 14.9 5.1 85951 -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 1.55 1.58 86.1 0.431 4.76 5.3 3910
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 3W71 1.55 29.88 85861 4295 92.98 0.138 0.1365 0.1375 0.1651 0.1658 RANDOM 14.8395
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 36.831 r_dihedral_angle_4_deg 18.515 r_dihedral_angle_3_deg 12.275 r_dihedral_angle_1_deg 6.857 r_angle_refined_deg 2.322 r_angle_other_deg 1.072 r_chiral_restr 0.14 r_bond_refined_d 0.025 r_gen_planes_refined 0.017 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.831 r_dihedral_angle_4_deg 18.515 r_dihedral_angle_3_deg 12.275 r_dihedral_angle_1_deg 6.857 r_angle_refined_deg 2.322 r_angle_other_deg 1.072 r_chiral_restr 0.14 r_bond_refined_d 0.025 r_gen_planes_refined 0.017 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4776 Nucleic Acid Atoms Solvent Atoms 728 Heterogen Atoms 195
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection