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Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor O-benzylhydroxylamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ILQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 200mM NaCl, 15%(w/v)PEG3350, 100mM bis-tris propane, 2%(v/v)DMSO
Crystal Properties Matthews coefficient Solvent content 2.91 57.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.025 α = 90 b = 104.507 β = 117.47 c = 87.301 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 291 PIXEL DECTRIS PILATUS 6M 2017-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033200 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.448 45.278 99.4 0.051 0.07 0.048 0.999 11.3 3.4 50829
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.52 0.464 0.643 0.443 0.852 3.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5ILQ 2.448 45.278 50809 2430 99.306 0.184 0.1821 0.1818 0.2231 0.2222 53.665
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] -1.472 0.097 4.451 -1.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.333 r_dihedral_angle_4_deg 19.132 r_dihedral_angle_3_deg 16.603 r_dihedral_angle_1_deg 7.037 r_lrange_it 6.423 r_lrange_other 6.383 r_scangle_it 4.292 r_scangle_other 4.273 r_mcangle_it 3.949 r_mcangle_other 3.949
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.333 r_dihedral_angle_4_deg 19.132 r_dihedral_angle_3_deg 16.603 r_dihedral_angle_1_deg 7.037 r_lrange_it 6.423 r_lrange_other 6.383 r_scangle_it 4.292 r_scangle_other 4.273 r_mcangle_it 3.949 r_mcangle_other 3.949 r_scbond_it 2.755 r_scbond_other 2.713 r_mcbond_it 2.516 r_mcbond_other 2.514 r_angle_refined_deg 1.87 r_angle_other_deg 1.347 r_symmetry_nbd_refined 0.486 r_nbd_other 0.443 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.204 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_other 0.116 r_ncsr_local_group_3 0.105 r_metal_ion_refined 0.099 r_ncsr_local_group_1 0.095 r_chiral_restr 0.089 r_ncsr_local_group_2 0.086 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8117 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASES phasing