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Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-4-129
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W1P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 277 0.1M Cacodylate, 13% PEG3350, 0.05M Hexaamminecobalt (III) Chloride, 1mM Oxonate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.41 α = 90 b = 71.957 β = 90 c = 129.733 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 MARMOSAIC 225 mm CCD 2009-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 1.78 50 93.8 0.078 16.8 4.7 58125 -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 1.78 1.84 88.6 0.419 5.84 4.5 5423
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3W1P 1.78 30.89 58001 2918 93.47 0.1463 0.1445 0.1582 0.1806 0.1917 RANDOM 16.213
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 37.961 r_dihedral_angle_4_deg 19.493 r_dihedral_angle_3_deg 12.433 r_dihedral_angle_1_deg 6.192 r_angle_refined_deg 2.094 r_angle_other_deg 1.02 r_chiral_restr 0.124 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.961 r_dihedral_angle_4_deg 19.493 r_dihedral_angle_3_deg 12.433 r_dihedral_angle_1_deg 6.192 r_angle_refined_deg 2.094 r_angle_other_deg 1.02 r_chiral_restr 0.124 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 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 617 Heterogen Atoms 219
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection