3DTD

Crystal structure of invasion associated protein b from bartonella henselae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8294200mM Trimethylamine N-oxide, 100MM TRIS-HCL, PH 8, 20% PEG MME 2000, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
2.6653.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.707α = 90
b = 139.951β = 90
c = 179.075γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMAR CCD 165 mm2008-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-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
12.355099.70.1246.4100682-0.552.606
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)
12.352.4398.70.920.55

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.352096697300099.270.235910.235010.26524RANDOM51.596
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]
0.44-0.22-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.9
r_dihedral_angle_4_deg20.964
r_dihedral_angle_3_deg17.548
r_scangle_it7.713
r_dihedral_angle_1_deg5.148
r_scbond_it4.879
r_mcangle_it4.345
r_mcbond_it2.662
r_angle_refined_deg1.249
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.9
r_dihedral_angle_4_deg20.964
r_dihedral_angle_3_deg17.548
r_scangle_it7.713
r_dihedral_angle_1_deg5.148
r_scbond_it4.879
r_mcangle_it4.345
r_mcbond_it2.662
r_angle_refined_deg1.249
r_nbtor_refined0.295
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.148
r_nbd_refined0.131
r_symmetry_hbond_refined0.108
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms13106
Nucleic Acid Atoms
Solvent Atoms416
Heterogen Atoms108

Software

Software
Software NamePurpose
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
RESOLVEmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing