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Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with SH-1-103
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W86 PDB ENTRY 3W86
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 2.3 46.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.934 α = 90 b = 71.484 β = 90 c = 129.646 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 2013-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90 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 1.43 50 97.4 0.07 9.8 6.5 114002 -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 1.43 1.45 96.1 0.417 4.94 6.4 5537
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 3W86 1.43 36.98 113919 5704 97.35 0.1549 0.1532 0.1517 0.1871 0.1857 RANDOM 13.85
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] -0.03 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.642 r_dihedral_angle_4_deg 19.003 r_dihedral_angle_3_deg 12.884 r_dihedral_angle_1_deg 6.614 r_scangle_it 5.079 r_scbond_it 3.593 r_angle_refined_deg 3.039 r_mcangle_it 2.075 r_mcbond_it 1.331 r_chiral_restr 0.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.642 r_dihedral_angle_4_deg 19.003 r_dihedral_angle_3_deg 12.884 r_dihedral_angle_1_deg 6.614 r_scangle_it 5.079 r_scbond_it 3.593 r_angle_refined_deg 3.039 r_mcangle_it 2.075 r_mcbond_it 1.331 r_chiral_restr 0.506 r_bond_refined_d 0.031 r_gen_planes_refined 0.021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4788 Nucleic Acid Atoms Solvent Atoms 821 Heterogen Atoms 421
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction