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X-ray crystal structure of a putative aspartate carbamoyltransferase from Trypanosoma cruzi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ML4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 pACT E10: 0.2 M sodium monobasic phosphate/potassium dibasic phosphate, 20% PEG 3350, protein at 18.47 mg/ml K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.98 α = 90 b = 134.55 β = 90 c = 159.46 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 RIGAKU SATURN 944+ 2012-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
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 2.1 50 97.1 0.127 8.93 105706 102675 -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 2.1 2.15 91.8 0.555 2.61
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 (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 1ML4 2.1 49.48 105706 97768 5134 97.17 0.19381 0.19146 0.1983 0.23807 0.2427 RANDOM 25.475
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] -1.16 -0.23 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.214 r_dihedral_angle_4_deg 18.857 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 6.219 r_angle_refined_deg 1.506 r_mcangle_it 1.004 r_angle_other_deg 0.808 r_scbond_it 0.682 r_mcbond_it 0.601 r_mcbond_other 0.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.214 r_dihedral_angle_4_deg 18.857 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 6.219 r_angle_refined_deg 1.506 r_mcangle_it 1.004 r_angle_other_deg 0.808 r_scbond_it 0.682 r_mcbond_it 0.601 r_mcbond_other 0.601 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13462 Nucleic Acid Atoms Solvent Atoms 868 Heterogen Atoms 45
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing