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Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase in complex with CMP
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 4000
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.52 α = 90 b = 69.3 β = 90 c = 116.44 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 2M 2015-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 1.98 58.22 99.3 0.059 10.5 4.6 13840
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 4ZCT 1.98 58.22 13840 710 99.3 0.20923 0.2073 0.2149 0.24713 0.2466 RANDOM 40.135
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 32.788 r_dihedral_angle_4_deg 15.769 r_dihedral_angle_3_deg 11.852 r_long_range_B_refined 6.617 r_long_range_B_other 6.615 r_dihedral_angle_1_deg 5.069 r_scangle_other 3.795 r_mcangle_it 3.147 r_mcangle_other 3.146 r_scbond_it 2.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.788 r_dihedral_angle_4_deg 15.769 r_dihedral_angle_3_deg 11.852 r_long_range_B_refined 6.617 r_long_range_B_other 6.615 r_dihedral_angle_1_deg 5.069 r_scangle_other 3.795 r_mcangle_it 3.147 r_mcangle_other 3.146 r_scbond_it 2.371 r_scbond_other 2.369 r_mcbond_it 1.967 r_mcbond_other 1.967 r_angle_refined_deg 1.104 r_angle_other_deg 0.673 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1023 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement PHASER phasing SCALA data scaling Coot model building XDS data reduction