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Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum in complex with BDA-14
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 2.87 57.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.26 α = 90 b = 90.016 β = 108.866 c = 136.942 γ = 90
Symmetry Space Group I 1 2 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 2021-02-19 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 2.55 45.599 98.1 0.045 0.063 0.045 0.998 9.4 1.9 43972
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 2.55 2.65 0.045 0.063 0.045 0.609 1.9
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 2.55 45.599 43971 2205 97.994 0.201 0.1991 0.2022 0.244 0.2438 76.47
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] 2.141 -5.08 -0.872 1.785
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.793 r_dihedral_angle_3_deg 19.644 r_dihedral_angle_4_deg 17.445 r_dihedral_angle_1_deg 7.891 r_lrange_it 5.952 r_lrange_other 5.925 r_mcangle_it 3.683 r_mcangle_other 3.682 r_scangle_it 3.361 r_scangle_other 3.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.793 r_dihedral_angle_3_deg 19.644 r_dihedral_angle_4_deg 17.445 r_dihedral_angle_1_deg 7.891 r_lrange_it 5.952 r_lrange_other 5.925 r_mcangle_it 3.683 r_mcangle_other 3.682 r_scangle_it 3.361 r_scangle_other 3.297 r_mcbond_it 2.217 r_mcbond_other 2.216 r_scbond_it 2.038 r_scbond_other 1.987 r_angle_refined_deg 1.779 r_angle_other_deg 1.269 r_nbd_other 0.268 r_nbd_refined 0.222 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.169 r_symmetry_nbd_refined 0.164 r_symmetry_xyhbond_nbd_other 0.154 r_ncsr_local_group_3 0.102 r_ncsr_local_group_1 0.099 r_ncsr_local_group_2 0.098 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_refined 0.056 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7824 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing