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Crystal structure of H. pylori referent strain in complex with PO4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other PNP from E. Coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 0.1 M Tris, 10 % PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.23 44.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.52 α = 90 b = 86.31 β = 90 c = 268.449 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2016-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.97957 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.73 134.22 87 28.88 11 133010
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.79 92 3.86 11.9
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 PNP from E. Coli 1.73 134.22 126978 6228 87.29 0.1859 0.1838 0.1831 0.2277 0.2264 RANDOM 17.1663
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.636 r_dihedral_angle_4_deg 18.791 r_dihedral_angle_3_deg 16.428 r_dihedral_angle_1_deg 6.722 r_mcangle_it 1.842 r_angle_refined_deg 1.726 r_scbond_it 1.685 r_mcbond_it 1.156 r_chiral_restr 0.167 r_bond_refined_d 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.636 r_dihedral_angle_4_deg 18.791 r_dihedral_angle_3_deg 16.428 r_dihedral_angle_1_deg 6.722 r_mcangle_it 1.842 r_angle_refined_deg 1.726 r_scbond_it 1.685 r_mcbond_it 1.156 r_chiral_restr 0.167 r_bond_refined_d 0.014 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10812 Nucleic Acid Atoms Solvent Atoms 1354 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling iMOSFLM data reduction PHENIX phasing