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Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi (Ligand-free form)
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, HANGING DROP 4.6 293 10% PEG 3350, 0.1 M acetate buffer pH 4.6, 0.2 M ammonium acetate, 0.01 M cobalt chloride and 3%
glycerol
Crystal Properties Matthews coefficient Solvent content 2.21 44.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.419 α = 69.56 b = 79.282 β = 82.9 c = 92.016 γ = 63.25
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE Bruker DIP-6040 2008-05-22 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 2.8 50 97.7 0.074 15.8 2.4 44850
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 2.8 2.9 98.4 0.389 4.4 2.4
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 1ML4 2.81 29.51 41411 2205 96.44 0.18214 0.1778 0.1813 0.26547 0.261 RANDOM 54.247
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] 0.6 -0.14 0.09 -0.03 0.12 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.696 r_dihedral_angle_4_deg 18.056 r_dihedral_angle_3_deg 17.87 r_long_range_B_refined 7.363 r_long_range_B_other 7.363 r_dihedral_angle_1_deg 7 r_scangle_other 5.233 r_mcangle_it 5.069 r_mcangle_other 5.069 r_mcbond_it 3.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.696 r_dihedral_angle_4_deg 18.056 r_dihedral_angle_3_deg 17.87 r_long_range_B_refined 7.363 r_long_range_B_other 7.363 r_dihedral_angle_1_deg 7 r_scangle_other 5.233 r_mcangle_it 5.069 r_mcangle_other 5.069 r_mcbond_it 3.223 r_mcbond_other 3.221 r_scbond_it 3.207 r_scbond_other 3.206 r_angle_refined_deg 1.559 r_angle_other_deg 1.01 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 13949 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing