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Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with phosphate (Pi).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JKQ
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, 3%
glycerol.
Crystal Properties Matthews coefficient Solvent content 2.5 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.42 α = 90 b = 158.607 β = 119.69 c = 89.2 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 300 mm CCD 2017-07-20 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 50 99.9 0.119 9.1 3.6 143565
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 2.03 100 0.56 2.5 3.4
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 6JKQ 2 20 127417 6710 93.4 0.18691 0.18504 0.1937 0.2226 0.23 RANDOM 27.803
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] -0.2 -0.11 0.84 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.477 r_dihedral_angle_4_deg 18.713 r_dihedral_angle_3_deg 14.479 r_dihedral_angle_1_deg 6.306 r_long_range_B_refined 4.573 r_long_range_B_other 4.561 r_scangle_other 2.978 r_mcangle_it 2.463 r_mcangle_other 2.463 r_scbond_it 1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.477 r_dihedral_angle_4_deg 18.713 r_dihedral_angle_3_deg 14.479 r_dihedral_angle_1_deg 6.306 r_long_range_B_refined 4.573 r_long_range_B_other 4.561 r_scangle_other 2.978 r_mcangle_it 2.463 r_mcangle_other 2.463 r_scbond_it 1.79 r_scbond_other 1.79 r_mcbond_it 1.517 r_mcbond_other 1.517 r_angle_refined_deg 1.399 r_angle_other_deg 0.954 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 14344 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing