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Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with oxonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 18% PEG 3350, 1mM Oxonic acid potassium salt, 0.25M Hexammine cobalt trichloride, 0.1M cacodylate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.22 44.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.359 α = 90 b = 71.828 β = 90 c = 123.639 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 100 CCD ADSC QUANTUM 210 2005-05-28 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 1.26 50 97.7 0.071 8.5 4.4 164341 160498 1
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 1.26 1.31 99.2 0.395 3.04 4.4 16102
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2E6A 1.26 29.91 1 164258 152389 8033 97.66 0.16625 0.16554 0.1635 0.1799 0.1783 RANDOM 9.858
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 36.936 r_dihedral_angle_4_deg 15.72 r_dihedral_angle_3_deg 10.876 r_dihedral_angle_1_deg 5.717 r_scangle_it 2.056 r_scbond_it 1.291 r_angle_refined_deg 1.168 r_mcangle_it 0.751 r_mcbond_it 0.475 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.936 r_dihedral_angle_4_deg 15.72 r_dihedral_angle_3_deg 10.876 r_dihedral_angle_1_deg 5.717 r_scangle_it 2.056 r_scbond_it 1.291 r_angle_refined_deg 1.168 r_mcangle_it 0.751 r_mcbond_it 0.475 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.284 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.083 r_chiral_restr 0.079 r_symmetry_hbond_refined 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4758 Nucleic Acid Atoms Solvent Atoms 799 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing