☰ Navigation Tabs
Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with TT2-3-063
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W7D PDB ENTRY 3W7D
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 2.34 47.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.224 α = 90 b = 72.009 β = 90 c = 129.644 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 2010-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2.4 50 93.6 0.104 8.9 4.2 24025 -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 2.4 2.44 96.6 0.254 5.01 4.1 1213
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 3W7D 2.4 48.18 23070 1180 89.8 0.1753 0.1717 0.1786 0.246 0.2512 RANDOM 29.9941
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 40.537 r_dihedral_angle_4_deg 20.74 r_dihedral_angle_3_deg 14.922 r_dihedral_angle_1_deg 6.997 r_angle_refined_deg 1.71 r_angle_other_deg 0.895 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.537 r_dihedral_angle_4_deg 20.74 r_dihedral_angle_3_deg 14.922 r_dihedral_angle_1_deg 6.997 r_angle_refined_deg 1.71 r_angle_other_deg 0.895 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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 253 Heterogen Atoms 225
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection