4XOT

Tailspike protein mutant E372Q of E. coli bacteriophage HK620 in complex with pentasaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XM3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.1 M Tris-HCl, 3.5 M Sodium formate
Crystal Properties
Matthews coefficientSolvent content
2.1642.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.179α = 90
b = 74.179β = 90
c = 174.678γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirrors2014-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.0643.6799.40.0580.0280.99913.95.2250525
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.061.08890.620.3570.6942.13.710927

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 REPLACEMENTTHROUGHOUT4XM31.0643.672505251251299.270.10650.10530.1296RANDOM11.576
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]
0.270.130.27-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.881
r_sphericity_free35.774
r_dihedral_angle_4_deg18.534
r_dihedral_angle_3_deg10.658
r_sphericity_bonded10.087
r_dihedral_angle_1_deg7.658
r_rigid_bond_restr6.01
r_angle_refined_deg1.938
r_mcangle_it1.788
r_mcbond_it1.393
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.881
r_sphericity_free35.774
r_dihedral_angle_4_deg18.534
r_dihedral_angle_3_deg10.658
r_sphericity_bonded10.087
r_dihedral_angle_1_deg7.658
r_rigid_bond_restr6.01
r_angle_refined_deg1.938
r_mcangle_it1.788
r_mcbond_it1.393
r_mcbond_other1.392
r_angle_other_deg0.978
r_chiral_restr0.133
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4532
Nucleic Acid Atoms
Solvent Atoms852
Heterogen Atoms103

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACphasing
ARPmodel building
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction