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Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor indole
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 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.714 α = 90 b = 103.822 β = 117.922 c = 87.067 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 2.946 44.8 99 0.089 0.123 0.086 0.995 9 3.3 28662
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 2.95 3.12 0.409 0.566 0.39 0.857 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 2.946 43.54 28645 1331 98.888 0.193 0.1911 0.1921 0.2385 0.2392 69.716
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] -4.222 0.636 7.994 -2.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.901 r_dihedral_angle_4_deg 18.929 r_dihedral_angle_3_deg 17.805 r_dihedral_angle_1_deg 7.616 r_lrange_it 7.434 r_lrange_other 7.432 r_mcangle_it 4.06 r_mcangle_other 4.059 r_scangle_it 3.946 r_scangle_other 3.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.901 r_dihedral_angle_4_deg 18.929 r_dihedral_angle_3_deg 17.805 r_dihedral_angle_1_deg 7.616 r_lrange_it 7.434 r_lrange_other 7.432 r_mcangle_it 4.06 r_mcangle_other 4.059 r_scangle_it 3.946 r_scangle_other 3.935 r_mcbond_other 2.477 r_mcbond_it 2.476 r_scbond_it 2.303 r_scbond_other 2.291 r_angle_refined_deg 1.715 r_angle_other_deg 1.24 r_nbd_other 0.426 r_symmetry_nbd_refined 0.398 r_symmetry_xyhbond_nbd_refined 0.246 r_nbd_refined 0.219 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.173 r_ncsr_local_group_3 0.108 r_ncsr_local_group_1 0.097 r_ncsr_local_group_2 0.097 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.023 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8172 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing