3IBX

Crystal structure of F47Y variant of TenA (HP1287) from Helicobacter pylori


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RD3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52770.1M Tris, 1.1M lithium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.728α = 90
b = 148.728β = 90
c = 233.566γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9794ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.412599.70.1538.69.95120051200
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.531000.463.710.27412

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2RD32.4785120050181254197.740.218310.217710.22957RANDOM20.875
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]
0.380.38-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.632
r_dihedral_angle_3_deg19.346
r_dihedral_angle_4_deg16.989
r_dihedral_angle_1_deg4.556
r_scangle_it2.119
r_scbond_it1.299
r_angle_refined_deg1.245
r_mcangle_it0.853
r_mcbond_it0.417
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.632
r_dihedral_angle_3_deg19.346
r_dihedral_angle_4_deg16.989
r_dihedral_angle_1_deg4.556
r_scangle_it2.119
r_scbond_it1.299
r_angle_refined_deg1.245
r_mcangle_it0.853
r_mcbond_it0.417
r_chiral_restr0.115
r_bond_refined_d0.01
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3553
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling