1TTW | pdb_00001ttw

Crystal structure of the Yersinia Pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.62981.8 M ammonium sulphate, 200 mM magnesium acetate, 100 mM CAPSO, 2% dioxane, 1.6 mM CHAPS, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.245

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.664α = 90
b = 63.664β = 90
c = 162.263γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.98397APS22-ID

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
12.3825850.06926.913919679162266.026
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)
12.382.4867.50.45410888

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUT2.3825229196791638898.830.245410.243120.260.292190.25RANDOM67.69
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]
0.610.30.61-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg11.704
r_scangle_it7.128
r_scbond_it4.59
r_angle_refined_deg3.518
r_mcangle_it3.376
r_mcbond_it1.897
r_angle_other_deg1.484
r_symmetry_hbond_refined0.514
r_nbd_refined0.285
r_symmetry_vdw_other0.284
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg11.704
r_scangle_it7.128
r_scbond_it4.59
r_angle_refined_deg3.518
r_mcangle_it3.376
r_mcbond_it1.897
r_angle_other_deg1.484
r_symmetry_hbond_refined0.514
r_nbd_refined0.285
r_symmetry_vdw_other0.284
r_nbd_other0.278
r_xyhbond_nbd_refined0.276
r_symmetry_vdw_refined0.259
r_chiral_restr0.193
r_nbtor_other0.128
r_bond_refined_d0.044
r_gen_planes_refined0.016
r_gen_planes_other0.012
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms993
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing