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Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with orotate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DOR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 18% PEG 3350, 1mM Sodium orotate, 0.25M Hexammine cobalt trichloride, 0.1M cacodylate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.248 α = 90 b = 71.881 β = 90 c = 123.574 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 2003-12-20 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 1.64 50 96.3 0.078 9.9 3.7 75068 72280 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 1.64 1.7 97.9 0.398 3.12 3.7 7243
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 2DOR 1.64 49.51 1 75135 68521 3653 96.06 0.16384 0.16231 0.1629 0.19248 0.1934 RANDOM 11.296
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 36.916 r_dihedral_angle_4_deg 17.739 r_dihedral_angle_3_deg 10.713 r_dihedral_angle_1_deg 5.555 r_scangle_it 3.128 r_scbond_it 1.916 r_angle_refined_deg 1.262 r_mcangle_it 1.079 r_mcbond_it 0.684 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.916 r_dihedral_angle_4_deg 17.739 r_dihedral_angle_3_deg 10.713 r_dihedral_angle_1_deg 5.555 r_scangle_it 3.128 r_scbond_it 1.916 r_angle_refined_deg 1.262 r_mcangle_it 1.079 r_mcbond_it 0.684 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.25 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.094 r_symmetry_hbond_refined 0.088 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4758 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing