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dutpase of helicobacter pylori 26695
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 0.1 M amino acid mix,0.1 M buffer system1 pH 6.5, 50% v/v precipitant mix4
Crystal Properties Matthews coefficient Solvent content 2.72 54.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.869 α = 90 b = 103.869 β = 90 c = 78.651 γ = 120
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 PILATUS3 6M 2021-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9805 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 89.95 100 0.129 0.99 18 19.3 32696
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 2.05 0.93
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 59.28 32675 1634 99.988 0.147 0.1447 0.1549 0.1812 0.1901 23.815
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] 0.467 0.233 0.467 -1.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.657 r_dihedral_angle_3_deg 13.271 r_dihedral_angle_2_deg 8.149 r_dihedral_angle_1_deg 6.577 r_lrange_it 6.048 r_lrange_other 6.003 r_scangle_it 4.978 r_scangle_other 4.977 r_scbond_other 3.259 r_scbond_it 3.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.657 r_dihedral_angle_3_deg 13.271 r_dihedral_angle_2_deg 8.149 r_dihedral_angle_1_deg 6.577 r_lrange_it 6.048 r_lrange_other 6.003 r_scangle_it 4.978 r_scangle_other 4.977 r_scbond_other 3.259 r_scbond_it 3.256 r_mcangle_it 2.824 r_mcangle_other 2.824 r_mcbond_it 1.989 r_mcbond_other 1.985 r_angle_refined_deg 1.442 r_angle_other_deg 0.483 r_symmetry_nbd_refined 0.267 r_nbd_refined 0.221 r_symmetry_nbd_other 0.199 r_chiral_restr_other 0.179 r_nbtor_refined 0.163 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.135 r_ncsr_local_group_2 0.102 r_ncsr_local_group_1 0.1 r_ncsr_local_group_3 0.098 r_symmetry_xyhbond_nbd_refined 0.09 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.071 r_metal_ion_refined 0.039 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3267 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing