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Adhesin domain of the type 1 HopQ of Helicobacter pylori strain G27
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.12M alcohols (0.02M 1,6-Hexanediol; 0.02M 1-Butanol; 0.02M 1,2-Propanediol; 0.02M 2-Propanol; 0.02M 1,4-Butanediol; 0.02M 1,3-Propanediol), 0.1 M Tris (base)/BICINE pH 8.5, 20% v/v PEG 500* MME; 10 % w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.7 α = 90 b = 57.7 β = 90.1 c = 285.6 γ = 90
Symmetry Space Group P 1 21 1
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 2014-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98 SOLEIL PROXIMA 1
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 2.6 49.4 99.7 0.147 0.993 7.3 4.7 55541
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 98.2 1.21 0.576 0.9 4.5
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 5F7K 2.6 49.4 55541 2924 99.83 0.20912 0.20768 0.2146 0.23617 0.239 RANDOM 65.023
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] 1.02 -0.77 0.81 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.66 r_dihedral_angle_3_deg 18.983 r_dihedral_angle_4_deg 10.248 r_long_range_B_refined 8.501 r_long_range_B_other 8.5 r_dihedral_angle_1_deg 7.482 r_scangle_other 6.397 r_mcangle_it 5.198 r_mcangle_other 5.198 r_scbond_it 3.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.66 r_dihedral_angle_3_deg 18.983 r_dihedral_angle_4_deg 10.248 r_long_range_B_refined 8.501 r_long_range_B_other 8.5 r_dihedral_angle_1_deg 7.482 r_scangle_other 6.397 r_mcangle_it 5.198 r_mcangle_other 5.198 r_scbond_it 3.931 r_scbond_other 3.931 r_mcbond_it 3.29 r_mcbond_other 3.288 r_angle_refined_deg 1.709 r_angle_other_deg 0.912 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10952 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing