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Thymidylate kinase of Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HJN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 60% v/v Tacsimate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.7 54.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.882 α = 90 b = 93.882 β = 90 c = 212.064 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS EIGER2 X 9M 2022-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.918 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.449 48.5 100 0.99 1.1 25.1 35800
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.449 2.98 0.83
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 48.44 31297 2382 99.964 0.22 0.2148 0.2163 0.2802 0.2815 58.007
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] -0.822 -0.822 1.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.895 r_dihedral_angle_6_deg 13.855 r_dihedral_angle_2_deg 9.965 r_lrange_it 8.828 r_lrange_other 8.828 r_scangle_it 6.47 r_scangle_other 6.469 r_dihedral_angle_1_deg 6.462 r_mcangle_it 5.758 r_mcangle_other 5.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.895 r_dihedral_angle_6_deg 13.855 r_dihedral_angle_2_deg 9.965 r_lrange_it 8.828 r_lrange_other 8.828 r_scangle_it 6.47 r_scangle_other 6.469 r_dihedral_angle_1_deg 6.462 r_mcangle_it 5.758 r_mcangle_other 5.758 r_scbond_it 4.165 r_scbond_other 4.165 r_mcbond_it 3.692 r_mcbond_other 3.674 r_angle_refined_deg 1.382 r_angle_other_deg 0.467 r_symmetry_nbd_refined 0.385 r_metal_ion_refined 0.275 r_nbd_refined 0.224 r_chiral_restr_other 0.209 r_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.178 r_nbd_other 0.156 r_symmetry_xyhbond_nbd_refined 0.14 r_dihedral_angle_other_2_deg 0.135 r_symmetry_xyhbond_nbd_other 0.089 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5483 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing