6G0X

TAILSPIKE PROTEIN OF E. COLI BACTERIOPHAGE HK620 IN COMPLEX WITH PENTASACCHARIDE


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1 M TRIS-HCL, 3.5 M SODIUMFORMIATE
Crystal Properties
Matthews coefficientSolvent content
2.1643.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.32α = 90
b = 74.32β = 90
c = 174.871γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-225MIRRORS2012-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.11.0BESSY14.1

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
11.4143.2198.60.07175.6107055
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)
11.411.4387.80.72824.4

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 REPLACEMENTTHROUGHOUT2vji1.4143.21107054534498.60.1490.1470.177RANDOM13.87
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]
0.210.10.21-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.593
r_dihedral_angle_4_deg16.652
r_dihedral_angle_3_deg10.736
r_dihedral_angle_1_deg7.486
r_angle_refined_deg1.914
r_angle_other_deg0.965
r_mcangle_it0.844
r_mcbond_it0.58
r_mcbond_other0.58
r_chiral_restr0.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.593
r_dihedral_angle_4_deg16.652
r_dihedral_angle_3_deg10.736
r_dihedral_angle_1_deg7.486
r_angle_refined_deg1.914
r_angle_other_deg0.965
r_mcangle_it0.844
r_mcbond_it0.58
r_mcbond_other0.58
r_chiral_restr0.174
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms4547
Nucleic Acid Atoms
Solvent Atoms804
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata reduction
Aimlessdata scaling
PHASERphasing