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Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-077
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W6Y PDB ENTRY 3W6Y
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 46.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.016 α = 90 b = 71.599 β = 90 c = 129.44 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 MARMOSAIC 225 mm CCD 2009-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.75 50 76.6 0.072 12.5 4.4 49701 -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 1.75 1.78 77.2 0.408 4.23 4 2445
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 3W6Y 1.75 34.03 49649 2534 76.47 0.1441 0.1414 0.1468 0.1947 0.1937 RANDOM 15.5647
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] 0.02 -0.61 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.309 r_dihedral_angle_4_deg 19.172 r_dihedral_angle_3_deg 12.836 r_dihedral_angle_1_deg 6.389 r_mcangle_it 2.249 r_angle_refined_deg 1.968 r_mcbond_it 1.438 r_mcbond_other 1.416 r_angle_other_deg 0.996 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.309 r_dihedral_angle_4_deg 19.172 r_dihedral_angle_3_deg 12.836 r_dihedral_angle_1_deg 6.389 r_mcangle_it 2.249 r_angle_refined_deg 1.968 r_mcbond_it 1.438 r_mcbond_other 1.416 r_angle_other_deg 0.996 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4776 Nucleic Acid Atoms Solvent Atoms 594 Heterogen Atoms 221
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection