2X85

Tailspike protein of E. coli bacteriophage HK620 in complex with hexasaccharide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293VAPOR DIFFUSION, HANGING DROP: PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH7.8, 2MM EDTA, 0.2M NACL. RESERVOIR: 100MM TRIS PH8.5, 3.5M NA-FORMIATE. DROPLET 1.5:1.5 MICROLITER, 0.3 MICROLITER 33MM HEXASACCHARIDE. TEMPERATURE 20 DEGREE CELSIUS.
Crystal Properties
Matthews coefficientSolvent content
2.1342.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.25α = 90
b = 74.25β = 90
c = 174.44γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDGLAS MIRROR2009-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.536.3190.40.0518.24.17734719.6
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)
11.51.54660.244.83.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2VJI1.537.1377347411290.40.166590.164910.19825RANDOM14.9
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]
0.610.310.61-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.543
r_dihedral_angle_4_deg15.821
r_dihedral_angle_3_deg11.096
r_dihedral_angle_1_deg7.119
r_scangle_it2.73
r_scbond_it2.01
r_angle_refined_deg1.33
r_mcangle_it1.221
r_angle_other_deg1.041
r_mcbond_it0.778
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.543
r_dihedral_angle_4_deg15.821
r_dihedral_angle_3_deg11.096
r_dihedral_angle_1_deg7.119
r_scangle_it2.73
r_scbond_it2.01
r_angle_refined_deg1.33
r_mcangle_it1.221
r_angle_other_deg1.041
r_mcbond_it0.778
r_mcbond_other0.255
r_chiral_restr0.091
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms4532
Nucleic Acid Atoms
Solvent Atoms691
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing