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Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with formamide bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1 M Bis-Tris pH 6.5, 2.1 M ammonium sulfate, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.72 66.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.61 α = 90 b = 81.713 β = 90 c = 94.538 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 CCD ADSC QUANTUM 315 Rh/Pt coated Si 2008-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.42 50 79.6 0.052 14.8 4.2 116723 92912 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.45 80 0.302 2.8 6171
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.42 48.83 92865 92865 4683 79.78 0.14 0.14 0.1387 0.1455 0.165 0.1699 RANDOM 16.6884
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] -0.11 -0.16 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.329 r_sphericity_free 17.359 r_dihedral_angle_3_deg 10.684 r_sphericity_bonded 8.026 r_scangle_it 7.629 r_dihedral_angle_4_deg 6.132 r_scbond_it 5.678 r_dihedral_angle_1_deg 5.603 r_mcangle_it 3.662 r_rigid_bond_restr 2.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.329 r_sphericity_free 17.359 r_dihedral_angle_3_deg 10.684 r_sphericity_bonded 8.026 r_scangle_it 7.629 r_dihedral_angle_4_deg 6.132 r_scbond_it 5.678 r_dihedral_angle_1_deg 5.603 r_mcangle_it 3.662 r_rigid_bond_restr 2.904 r_mcbond_it 2.772 r_angle_refined_deg 1.492 r_mcbond_other 1.463 r_angle_other_deg 0.921 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2482 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 46
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction EPMR phasing