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Structure of Helicobacter pylori Csd6 in the ligand-free state
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 1.5%(v/v) Tacsimate (pH 7.0), 22%(w/v) PEG 3350, 100mM sodium-HEPES
Crystal Properties Matthews coefficient Solvent content 2.401 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.963 α = 90 b = 91.028 β = 90 c = 127.799 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 270 2012-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0 Photon Factory BL-1A
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 2.03 50 98.3 0.095 25 4.82 47555
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 2.03 2.07 98.1 0.47 3 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.03 30 45088 2396 98.01 0.19825 0.19572 0.2033 0.24813 0.2513 RANDOM 40.671
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] 2.21 -1.52 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.661 r_dihedral_angle_4_deg 16.191 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 6.453 r_long_range_B_refined 6.184 r_long_range_B_other 6.175 r_scangle_other 4.552 r_mcangle_it 3.368 r_mcangle_other 3.367 r_scbond_it 2.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.661 r_dihedral_angle_4_deg 16.191 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 6.453 r_long_range_B_refined 6.184 r_long_range_B_other 6.175 r_scangle_other 4.552 r_mcangle_it 3.368 r_mcangle_other 3.367 r_scbond_it 2.823 r_scbond_other 2.823 r_mcbond_it 2.313 r_mcbond_other 2.311 r_angle_refined_deg 1.325 r_angle_other_deg 0.731 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 5248 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DENZO data reduction HKL-2000 data scaling PHENIX phasing