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Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with dihydroorotate
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 2.23 44.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.443 α = 90 b = 71.944 β = 90 c = 123.852 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 1.38 50 97.5 0.084 10.5 4.6 126103 122937 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 1.38 1.43 98.9 0.396 4.26 4.6 12338
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 1.38 29.99 1 126157 116503 6159 97.23 0.16919 0.16846 0.167 0.18286 0.1808 RANDOM 8.754
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 37.429 r_dihedral_angle_4_deg 17.26 r_dihedral_angle_3_deg 10.926 r_dihedral_angle_1_deg 5.513 r_scangle_it 2.356 r_scbond_it 1.482 r_angle_refined_deg 1.198 r_mcangle_it 0.873 r_mcbond_it 0.559 r_symmetry_hbond_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.429 r_dihedral_angle_4_deg 17.26 r_dihedral_angle_3_deg 10.926 r_dihedral_angle_1_deg 5.513 r_scangle_it 2.356 r_scbond_it 1.482 r_angle_refined_deg 1.198 r_mcangle_it 0.873 r_mcbond_it 0.559 r_symmetry_hbond_refined 0.33 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4763 Nucleic Acid Atoms Solvent Atoms 632 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing