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Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with succinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E6A PDB ENTRY 2E6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 18% PEG 3350, 1mM Oxonic acid potassium salt, 0.25M hexaammine cobalt trichloride, 0.1M cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.2 44.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.154 α = 90 b = 71.766 β = 90 c = 123.4 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 2005-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 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 1.38 50 94.9 0.06 9 5.2 125392 118965 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 69.5 0.33 2.62 3.4 12383
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 PDB ENTRY 2E6A 1.38 50 1 125392 112910 5980 95.51 0.16612 0.16524 0.1642 0.18277 0.1819 RANDOM 12.021
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 37.232 r_dihedral_angle_4_deg 17.436 r_dihedral_angle_3_deg 10.446 r_dihedral_angle_1_deg 5.688 r_scangle_it 2.288 r_scbond_it 1.471 r_angle_refined_deg 1.192 r_mcangle_it 0.81 r_mcbond_it 0.507 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.232 r_dihedral_angle_4_deg 17.436 r_dihedral_angle_3_deg 10.446 r_dihedral_angle_1_deg 5.688 r_scangle_it 2.288 r_scbond_it 1.471 r_angle_refined_deg 1.192 r_mcangle_it 0.81 r_mcbond_it 0.507 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.309 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.099 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4758 Nucleic Acid Atoms Solvent Atoms 695 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing