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dUTPase of helicobacter pylori 26695
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MBQ 3MBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 MORPHEUS H4 condition:0.1 M Amino acid mix, 0.1 M buffer system pH 6.5, 50% V/V precipitant mix 4
Crystal Properties Matthews coefficient Solvent content 2.36 47.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.36 α = 90 b = 102.36 β = 90 c = 78.37 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 PILATUS 6M 2018-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9791 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 2.5 58.7 100 0.99 18.7 46.3 16291
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 2.5 2.6 0.833
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3MBQ 2.5 58.7 16273 1092 99.969 0.179 0.175 0.1817 0.2384 0.2332 47.122
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] -0.165 -0.082 -0.165 0.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.384 r_dihedral_angle_6_deg 15.109 r_lrange_other 7.5 r_lrange_it 7.497 r_dihedral_angle_1_deg 7.184 r_dihedral_angle_2_deg 6.519 r_scangle_it 5.812 r_scangle_other 5.81 r_mcangle_it 3.954 r_mcangle_other 3.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.384 r_dihedral_angle_6_deg 15.109 r_lrange_other 7.5 r_lrange_it 7.497 r_dihedral_angle_1_deg 7.184 r_dihedral_angle_2_deg 6.519 r_scangle_it 5.812 r_scangle_other 5.81 r_mcangle_it 3.954 r_mcangle_other 3.954 r_scbond_it 3.605 r_scbond_other 3.589 r_mcbond_it 2.53 r_mcbond_other 2.513 r_angle_refined_deg 1.339 r_angle_other_deg 0.447 r_symmetry_nbd_refined 0.389 r_symmetry_xyhbond_nbd_refined 0.346 r_nbd_other 0.245 r_nbd_refined 0.203 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.124 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.058 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 2981 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing