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Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase in complex with phosphocholine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20% PEG 4k
Crystal Properties Matthews coefficient Solvent content 2.49 50.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.62 α = 90 b = 69.57 β = 90 c = 117.86 γ = 90
Symmetry Space Group I 2 2 2
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-F 2015-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972957 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.8 46.51 99.63 0.054 14.3 6.4 18719
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 THROUGHOUT 4ZCT 1.8 46.51 18719 927 99.63 0.17892 0.17641 0.1844 0.2322 0.2452 RANDOM 47.198
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] -0.09 0.07 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.703 r_sphericity_free 26.232 r_dihedral_angle_4_deg 21.918 r_dihedral_angle_3_deg 12.612 r_sphericity_bonded 9.456 r_dihedral_angle_1_deg 6.774 r_long_range_B_refined 4.354 r_long_range_B_other 4.352 r_scangle_other 3.859 r_mcangle_it 3.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.703 r_sphericity_free 26.232 r_dihedral_angle_4_deg 21.918 r_dihedral_angle_3_deg 12.612 r_sphericity_bonded 9.456 r_dihedral_angle_1_deg 6.774 r_long_range_B_refined 4.354 r_long_range_B_other 4.352 r_scangle_other 3.859 r_mcangle_it 3.76 r_mcangle_other 3.757 r_mcbond_other 3.606 r_mcbond_it 3.602 r_scbond_it 3.178 r_scbond_other 3.175 r_rigid_bond_restr 1.992 r_angle_refined_deg 1.218 r_angle_other_deg 1.076 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1040 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data scaling Coot model building