2VBM

Tailspike protein of bacteriophage Sf6 complexed with tetrasaccharide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293VAPOR DIFFUSION HANGING DROP, 20 DEGR. CELSIUS; DROP: 3 MICROL RESERVOIR AND 3 MICROL PROTEIN SOLUTION; RESERVOIR: 0.1M MES, PH6.5, 16% PEG8000, 20MM MNCL2; PROTEIN: 10MG/ML, 10MM NA-PHOSPHATE,PH7.0, OCTASACCHARIDE CONCENTRATION/PROTEIN CONCENTATION 10:1; CRYOCONDITION: 0.1M MES, PH6.5, 25% PEG8000, 20MM MNCL2, 15% ETHYLENGLYCOL
Crystal Properties
Matthews coefficientSolvent content
2.957.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.358α = 90
b = 95.358β = 90
c = 182.765γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2005-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1247.799.70.0617.44.93964117.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0797.20.2274

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VBK247.6739641211099.80.1920.190.232RANDOM20.2
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]
0.360.180.36-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.978
r_dihedral_angle_4_deg12.96
r_dihedral_angle_3_deg12.676
r_dihedral_angle_1_deg6.767
r_scangle_it2.843
r_scbond_it2.086
r_angle_refined_deg1.362
r_mcangle_it1.108
r_mcbond_it0.826
r_angle_other_deg0.766
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.978
r_dihedral_angle_4_deg12.96
r_dihedral_angle_3_deg12.676
r_dihedral_angle_1_deg6.767
r_scangle_it2.843
r_scbond_it2.086
r_angle_refined_deg1.362
r_mcangle_it1.108
r_mcbond_it0.826
r_angle_other_deg0.766
r_symmetry_vdw_other0.221
r_nbd_other0.187
r_nbd_refined0.181
r_nbtor_refined0.168
r_symmetry_hbond_refined0.149
r_symmetry_vdw_refined0.144
r_xyhbond_nbd_refined0.136
r_nbtor_other0.095
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3821
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing