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Crystal structure of Aspartate Transcarbamoylase from Plasmodium falciparum (PfATC) with bound citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other PfATC-Met3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Potassium citrate tribasic monohydrate, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.45 α = 90 b = 107.29 β = 117.46 c = 87.32 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 100 PIXEL DECTRIS PILATUS 2M 2015-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.21 45.1 97.7 0.108 0.112 0.984 5 2.9 69115
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.29 83.8 0.8 0.8 2.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PfATC-Met3 2.21 45.1 65645 3470 97.64 0.18224 0.17957 0.1864 0.23398 0.2351 RANDOM 51.616
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.181 r_dihedral_angle_4_deg 22.89 r_dihedral_angle_3_deg 17.153 r_long_range_B_refined 8.948 r_long_range_B_other 8.946 r_dihedral_angle_1_deg 7.338 r_scangle_other 6.936 r_mcangle_it 5.719 r_mcangle_other 5.718 r_scbond_it 4.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.181 r_dihedral_angle_4_deg 22.89 r_dihedral_angle_3_deg 17.153 r_long_range_B_refined 8.948 r_long_range_B_other 8.946 r_dihedral_angle_1_deg 7.338 r_scangle_other 6.936 r_mcangle_it 5.719 r_mcangle_other 5.718 r_scbond_it 4.561 r_scbond_other 4.515 r_mcbond_it 3.863 r_mcbond_other 3.857 r_angle_refined_deg 2.248 r_angle_other_deg 1.188 r_chiral_restr 0.132 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8200 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling MOLREP phasing