2R62

Crystal structure of Helicobacter pylori ATP dependent protease, FtsH


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82980.1M Tris-HCl pH 8.0, 17%(w/v) PEG 4000, 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.754.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.217α = 90
b = 141.217β = 90
c = 54.659γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 3152006-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.250980.0650.06541.13.989638963
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)RedundancyNumber Unique Reflections (All)
13.23.3899.30.3910.3913.73.7988

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1IXZ3.3508963896346198.850.282830.282830.280290.33596RANDOM142.722
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]
-3.75-1.88-3.755.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.298
r_dihedral_angle_3_deg20.687
r_mcangle_it18.79
r_dihedral_angle_4_deg18.004
r_mcbond_it14.107
r_dihedral_angle_1_deg6.572
r_angle_refined_deg1.799
r_scangle_it1.695
r_scbond_it0.983
r_symmetry_hbond_refined0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.298
r_dihedral_angle_3_deg20.687
r_mcangle_it18.79
r_dihedral_angle_4_deg18.004
r_mcbond_it14.107
r_dihedral_angle_1_deg6.572
r_angle_refined_deg1.799
r_scangle_it1.695
r_scbond_it0.983
r_symmetry_hbond_refined0.36
r_nbtor_refined0.331
r_nbd_refined0.314
r_symmetry_vdw_refined0.296
r_xyhbond_nbd_refined0.228
r_chiral_restr0.102
r_bond_refined_d0.019
r_gen_planes_refined0.007
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 AtomsNumber
Protein Atoms3802
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing