2X6X

Tailspike protein mutant D339N 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.RERVOIR: 100MM TRIS PH8.5,3.5M NA-FORMIATE. DROPLET 1.5:1.5 MICRO LITER, 0.3 MICRO LITER 33MM HEXASACCHARIDE.TEMPERATURE 20 DEGREE CELSIUS.
Crystal Properties
Matthews coefficientSolvent content
2.1242.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.23α = 90
b = 74.23β = 90
c = 174.29γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHGLAS 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
11.4837.1298.60.0517.14.78769722.4
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)
11.481.5271.50.472.93.8

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 2VJI1.4837.1287697463398.640.158940.157530.18537RANDOM17.494
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]
0.740.370.74-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.621
r_dihedral_angle_4_deg16.904
r_dihedral_angle_3_deg11.26
r_dihedral_angle_1_deg6.897
r_scangle_it3.088
r_scbond_it2.094
r_angle_refined_deg1.375
r_mcangle_it1.257
r_angle_other_deg1.131
r_mcbond_it0.724
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.621
r_dihedral_angle_4_deg16.904
r_dihedral_angle_3_deg11.26
r_dihedral_angle_1_deg6.897
r_scangle_it3.088
r_scbond_it2.094
r_angle_refined_deg1.375
r_mcangle_it1.257
r_angle_other_deg1.131
r_mcbond_it0.724
r_mcbond_other0.214
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms4536
Nucleic Acid Atoms
Solvent Atoms572
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing