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Crystal structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with mutated active site (R109A/K138A) and N-carbamoyl-L-phosphate bound
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 293 0.2M Potassium citrate tribasic monohydrate
20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.06 59.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.001 α = 90 b = 89.715 β = 122.17 c = 121.642 γ = 90
Symmetry Space Group C 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 100 PIXEL DECTRIS PILATUS 6M 2016-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.5 57.61 97.6 0.066 0.999 12.95 3.16 46404 1.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 94 0.957 0.619 3.21
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ilq 2.5 57.61 43356 2399 98.01 0.207 0.2042 0.2578 0.2478 RANDOM 65.452
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] -0.15 -0.02 0.13 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.932 r_dihedral_angle_3_deg 20.426 r_dihedral_angle_4_deg 18.786 r_dihedral_angle_1_deg 9.004 r_mcangle_it 5.477 r_mcbond_it 3.421 r_mcbond_other 3.42 r_angle_other_deg 2.412 r_angle_refined_deg 1.946 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.932 r_dihedral_angle_3_deg 20.426 r_dihedral_angle_4_deg 18.786 r_dihedral_angle_1_deg 9.004 r_mcangle_it 5.477 r_mcbond_it 3.421 r_mcbond_other 3.42 r_angle_other_deg 2.412 r_angle_refined_deg 1.946 r_chiral_restr 0.088 r_bond_other_d 0.035 r_bond_refined_d 0.01 r_gen_planes_other 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7870 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction EDNA data collection DIMPLE model building