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Helicobacter pylori adhesin HopQ type I bound to the N-terminal domain of human CEACAM1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LP2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Condition B3 of the Morpheus HT-96 screen (Molecular Dimensions)(0.09 M Halogens mix (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (1.0M Imidazole; MES monohydrate (acid); pH 6.5), 50 % v/v Precipitant Mix 3 (40% v/v Glycerol; 20% w/v PEG 4000)
Crystal Properties Matthews coefficient Solvent content 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.43 α = 90 b = 94.43 β = 90 c = 119.7 γ = 120
Symmetry Space Group P 32 2 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 2016-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.98 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.8 67.52 100 0.147 0.047 0.998 13.6 10.5 15692 73.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 99.6 0.538 0.628 1.6 10.7
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 5LP2 2.8 67.52 14860 807 99.91 0.20471 0.20131 0.2057 0.26328 0.2605 RANDOM 71.153
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] 0.64 0.32 0.64 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.573 r_dihedral_angle_3_deg 18.261 r_dihedral_angle_4_deg 13.315 r_dihedral_angle_1_deg 7.102 r_long_range_B_refined 5.683 r_long_range_B_other 5.682 r_scangle_other 3.806 r_mcangle_it 3.156 r_mcangle_other 3.156 r_scbond_it 2.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.573 r_dihedral_angle_3_deg 18.261 r_dihedral_angle_4_deg 13.315 r_dihedral_angle_1_deg 7.102 r_long_range_B_refined 5.683 r_long_range_B_other 5.682 r_scangle_other 3.806 r_mcangle_it 3.156 r_mcangle_other 3.156 r_scbond_it 2.315 r_scbond_other 2.314 r_mcbond_it 1.943 r_mcbond_other 1.942 r_angle_refined_deg 1.457 r_angle_other_deg 0.782 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3271 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing