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Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum in complex with BDA-04
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 2.18 43.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.065 α = 89.981 b = 87.36 β = 90.036 c = 104.636 γ = 117.724
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 2019-07-13 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 2.292 62.192 97.1 0.056 0.079 0.056 0.992 9.4 1.7 117783
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 2.3 2.34 0.303 0.429 0.303 0.931 1.8
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 2.292 62.192 117672 6216 95.99 0.165 0.1636 0.1636 0.1914 0.1913 54.772
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] 3.212 -1.142 -3.002 -3.233 2.366 0.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.162 r_dihedral_angle_4_deg 24.94 r_dihedral_angle_3_deg 18.767 r_dihedral_angle_1_deg 8.087 r_lrange_it 7.021 r_lrange_other 7.017 r_mcangle_it 5.232 r_mcangle_other 5.232 r_scangle_it 5.04 r_scangle_other 5.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.162 r_dihedral_angle_4_deg 24.94 r_dihedral_angle_3_deg 18.767 r_dihedral_angle_1_deg 8.087 r_lrange_it 7.021 r_lrange_other 7.017 r_mcangle_it 5.232 r_mcangle_other 5.232 r_scangle_it 5.04 r_scangle_other 5.007 r_mcbond_it 3.825 r_mcbond_other 3.825 r_scbond_it 3.713 r_scbond_other 3.659 r_angle_refined_deg 2.037 r_angle_other_deg 1.392 r_symmetry_xyhbond_nbd_refined 0.334 r_xyhbond_nbd_refined 0.256 r_nbd_other 0.239 r_nbd_refined 0.228 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.172 r_symmetry_xyhbond_nbd_other 0.141 r_ncsr_local_group_7 0.104 r_ncsr_local_group_6 0.103 r_ncsr_local_group_9 0.103 r_ncsr_local_group_11 0.103 r_ncsr_local_group_10 0.1 r_ncsr_local_group_1 0.099 r_ncsr_local_group_5 0.099 r_ncsr_local_group_3 0.098 r_ncsr_local_group_4 0.098 r_ncsr_local_group_13 0.098 r_chiral_restr 0.097 r_ncsr_local_group_15 0.097 r_ncsr_local_group_2 0.096 r_ncsr_local_group_14 0.095 r_ncsr_local_group_8 0.093 r_symmetry_nbtor_other 0.087 r_ncsr_local_group_12 0.086 r_metal_ion_refined 0.026 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16344 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing