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Crystal structure of a Type IV Secretion System Component CagX in Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.1M Tris-HCl, 27% PEG4K, 10% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.09 41.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.08 α = 90 b = 61.62 β = 90.23 c = 48.42 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 CCD ADSC QUANTUM 315 2015-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AichiSR BEAMLINE BL2S1 0.97946 AichiSR BL2S1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.4 38.07 91.7 0.05 0.997 12.3 3.7 34978
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.44 56 0.347 0.803 3 3.4
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 3jqo 1.4 38.07 33259 1699 90.5 0.20255 0.20025 0.1969 0.24887 0.2456 RANDOM 15.553
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] -3.2 -0.32 14.02 -10.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.337 r_dihedral_angle_3_deg 17.081 r_dihedral_angle_4_deg 14.962 r_dihedral_angle_1_deg 6.482 r_long_range_B_refined 4.351 r_mcangle_it 2.425 r_scbond_it 1.882 r_angle_refined_deg 1.712 r_mcbond_it 1.676 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.337 r_dihedral_angle_3_deg 17.081 r_dihedral_angle_4_deg 14.962 r_dihedral_angle_1_deg 6.482 r_long_range_B_refined 4.351 r_mcangle_it 2.425 r_scbond_it 1.882 r_angle_refined_deg 1.712 r_mcbond_it 1.676 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1666 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing HKL-2000 data scaling MOLREP phasing HKL data scaling