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Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-bromoorotate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 298 0.1M Cacodylate, 13% PEG3350, 0.05M Hexaamminecobalt (III) Chloride, 1mM Oxonate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.341 α = 90 b = 71.912 β = 90 c = 123.849 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 ADSC QUANTUM 210 2007-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.9 29.95 99.8 0.103 5.9 4.6 48557 48456 -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 1.9 1.97 0.328 4 4.4 4758
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3W1A 1.9 29.95 46033 46033 2455 99.61 0.14517 0.14517 0.14316 0.1449 0.18272 0.1845 RANDOM 10.688
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 37.872 r_dihedral_angle_4_deg 19.291 r_dihedral_angle_3_deg 12.587 r_dihedral_angle_1_deg 6.374 r_angle_refined_deg 1.982 r_angle_other_deg 0.968 r_chiral_restr 0.125 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.872 r_dihedral_angle_4_deg 19.291 r_dihedral_angle_3_deg 12.587 r_dihedral_angle_1_deg 6.374 r_angle_refined_deg 1.982 r_angle_other_deg 0.968 r_chiral_restr 0.125 r_bond_refined_d 0.021 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 639 Heterogen Atoms 129
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling