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Crystal structure of cytidylyltransferase from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VIC PDB entry 1vic
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 297 1M tri-Na citrate, 0.1M sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.42 49.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.928 α = 82.73 b = 68.209 β = 74.19 c = 71.476 γ = 76.97
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 2010-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
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 1.753 68.606 94.42 0.041 0.041 22.75 1.2 172421 104474 -5
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) 1.8 1.83 92.9 0.301 1.96 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1vic 1.75 25.06 93730 93730 4919 100 0.19979 0.19806 0.1972 0.23209 0.2308 RANDOM 37.235
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] -0.42 -1.05 0.56 0.36 -1.6 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.874 r_dihedral_angle_4_deg 15.395 r_dihedral_angle_3_deg 13.86 r_dihedral_angle_1_deg 9.818 r_scangle_it 2.654 r_scbond_it 1.557 r_angle_refined_deg 1.228 r_mcangle_it 0.882 r_mcbond_it 0.475 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.874 r_dihedral_angle_4_deg 15.395 r_dihedral_angle_3_deg 13.86 r_dihedral_angle_1_deg 9.818 r_scangle_it 2.654 r_scbond_it 1.557 r_angle_refined_deg 1.228 r_mcangle_it 0.882 r_mcbond_it 0.475 r_chiral_restr 0.086 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7768 Nucleic Acid Atoms Solvent Atoms 690 Heterogen Atoms 1
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling