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Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with fumarate
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 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.282 α = 90 b = 71.88 β = 90 c = 123.612 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 Bruker DIP-6040 2005-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 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 1.94 50 99.9 0.099 12.8 6.1 45924 45874 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 1.94 2.01 100 0.244 8.19 6.1 4518
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 1.94 46.88 1 45903 43381 2302 99.52 0.15796 0.1558 0.1586 0.19974 0.2015 RANDOM 9.659
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 37.967 r_dihedral_angle_4_deg 20.267 r_dihedral_angle_3_deg 11.95 r_dihedral_angle_1_deg 5.636 r_scangle_it 3.661 r_scbond_it 2.309 r_angle_refined_deg 1.438 r_mcangle_it 1.245 r_mcbond_it 0.82 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.967 r_dihedral_angle_4_deg 20.267 r_dihedral_angle_3_deg 11.95 r_dihedral_angle_1_deg 5.636 r_scangle_it 3.661 r_scbond_it 2.309 r_angle_refined_deg 1.438 r_mcangle_it 1.245 r_mcbond_it 0.82 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.308 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4758 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing