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Human CTP: Phosphoethanolamine Cytidylyltransferase in complex with CTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ELB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 293 17% PEG3350, 0.2M magnesium formate, 0.1M HEPES, 0.01M CTP, 0.01M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.39 α = 90 b = 73.39 β = 90 c = 140.03 γ = 90
Symmetry Space Group P 41 21 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 CCD ADSC QUANTUM 4 2008-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933300 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 40 99.7 0.131 0.129 16.4 9.2 11119 11119
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 2.7 2.8 99.6 0.526 4.6 9.5
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 3ELB 2.7 39.37 10517 553 99.73 0.19477 0.191 0.193 0.26417 0.2648 RANDOM 34.017
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] 2.04 2.04 -4.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.647 r_dihedral_angle_4_deg 16.443 r_dihedral_angle_3_deg 15.936 r_dihedral_angle_1_deg 5.991 r_long_range_B_other 5.413 r_long_range_B_refined 5.411 r_scangle_other 3.611 r_mcangle_it 3.118 r_mcangle_other 3.117 r_scbond_it 2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.647 r_dihedral_angle_4_deg 16.443 r_dihedral_angle_3_deg 15.936 r_dihedral_angle_1_deg 5.991 r_long_range_B_other 5.413 r_long_range_B_refined 5.411 r_scangle_other 3.611 r_mcangle_it 3.118 r_mcangle_other 3.117 r_scbond_it 2.14 r_scbond_other 2.139 r_mcbond_it 1.873 r_mcbond_other 1.87 r_angle_refined_deg 1.512 r_angle_other_deg 0.785 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 2445 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing