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Crystal structure of Helicobacter pylori ATP dependent protease, FtsH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IXZ PDB entry 1IXZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.1M Tris-HCl pH 8.0, 17%(w/v) PEG 4000, 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.217 α = 90 b = 141.217 β = 90 c = 54.659 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD ADSC QUANTUM 315 2006-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.2 50 98 0.065 0.065 41.1 3.9 8963 8963
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.38 99.3 0.391 0.391 3.7 3.7 988
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 1IXZ 3.3 50 8963 8963 461 98.85 0.28283 0.28283 0.28029 0.2792 0.33596 0.3344 RANDOM 142.722
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] -3.75 -1.88 -3.75 5.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.298 r_dihedral_angle_3_deg 20.687 r_mcangle_it 18.79 r_dihedral_angle_4_deg 18.004 r_mcbond_it 14.107 r_dihedral_angle_1_deg 6.572 r_angle_refined_deg 1.799 r_scangle_it 1.695 r_scbond_it 0.983 r_symmetry_hbond_refined 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.298 r_dihedral_angle_3_deg 20.687 r_mcangle_it 18.79 r_dihedral_angle_4_deg 18.004 r_mcbond_it 14.107 r_dihedral_angle_1_deg 6.572 r_angle_refined_deg 1.799 r_scangle_it 1.695 r_scbond_it 0.983 r_symmetry_hbond_refined 0.36 r_nbtor_refined 0.331 r_nbd_refined 0.314 r_symmetry_vdw_refined 0.296 r_xyhbond_nbd_refined 0.228 r_chiral_restr 0.102 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3802 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing