☰ Navigation Tabs
Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor 2-phenylethan-1-amine
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 2.86 56.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.85 α = 90 b = 104.368 β = 117.525 c = 87.048 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 2.349 45.131 98.4 0.042 0.058 0.04 0.999 16.4 3.4 56561
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 2.35 2.41 0.459 0.642 0.448 0.824 3.2
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 2.349 45.131 56531 2711 98.264 0.219 0.2167 0.216 0.2723 0.271 59.972
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] -1.848 0.865 3.492 -1.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.374 r_dihedral_angle_3_deg 18.542 r_dihedral_angle_4_deg 18.256 r_dihedral_angle_1_deg 7.349 r_lrange_it 6.692 r_lrange_other 6.678 r_mcangle_it 4.424 r_mcangle_other 4.424 r_scangle_it 4.36 r_scangle_other 4.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.374 r_dihedral_angle_3_deg 18.542 r_dihedral_angle_4_deg 18.256 r_dihedral_angle_1_deg 7.349 r_lrange_it 6.692 r_lrange_other 6.678 r_mcangle_it 4.424 r_mcangle_other 4.424 r_scangle_it 4.36 r_scangle_other 4.34 r_scbond_it 2.875 r_mcbond_it 2.855 r_mcbond_other 2.855 r_scbond_other 2.844 r_angle_refined_deg 1.832 r_angle_other_deg 1.234 r_symmetry_xyhbond_nbd_refined 0.44 r_nbd_other 0.275 r_symmetry_nbd_refined 0.23 r_nbd_refined 0.223 r_symmetry_nbd_other 0.198 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.171 r_ncsr_local_group_3 0.121 r_ncsr_local_group_1 0.116 r_ncsr_local_group_2 0.116 r_xyhbond_nbd_other 0.115 r_metal_ion_refined 0.09 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.081 r_symmetry_xyhbond_nbd_other 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8117 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASES phasing