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Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase in complex with CDP-choline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 293 0.2M NaF, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.01 59.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.631 α = 90 b = 149.132 β = 90 c = 175.598 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 2014-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979338 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 2.45 113.67 99.63 0.32 0.2 9.35 52521
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 3HL4 2.45 113.67 52521 2808 99.63 0.18325 0.18059 0.1879 0.23413 0.2344 RANDOM 44.051
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] 0.07 -0.09 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.454 r_dihedral_angle_4_deg 21.093 r_dihedral_angle_3_deg 15.972 r_long_range_B_refined 9.192 r_long_range_B_other 9.192 r_dihedral_angle_1_deg 7.022 r_scangle_other 6.697 r_mcangle_it 6.127 r_mcangle_other 6.127 r_scbond_it 4.364
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.454 r_dihedral_angle_4_deg 21.093 r_dihedral_angle_3_deg 15.972 r_long_range_B_refined 9.192 r_long_range_B_other 9.192 r_dihedral_angle_1_deg 7.022 r_scangle_other 6.697 r_mcangle_it 6.127 r_mcangle_other 6.127 r_scbond_it 4.364 r_scbond_other 4.363 r_mcbond_it 4.065 r_mcbond_other 4.065 r_angle_refined_deg 1.97 r_angle_other_deg 1.134 r_chiral_restr 0.11 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.004 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 6806 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building