4XOR

Tailspike protein double mutant D339N/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
2.1642.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.257α = 90
b = 74.257β = 90
c = 174.512γ = 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 14.10.91841BESSY14.1

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
11.543.1499.90.0730.0320.99918.4690151
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)
11.51.53980.7430.3640.7312.15.14325

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 REPLACEMENTTHROUGHOUT4XM31.543.1490151450499.950.14380.14250.1685RANDOM15.108
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]
0.190.10.19-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.337
r_dihedral_angle_4_deg16.845
r_dihedral_angle_3_deg11.345
r_dihedral_angle_1_deg7.445
r_angle_refined_deg1.795
r_mcangle_it0.96
r_angle_other_deg0.916
r_mcbond_it0.668
r_mcbond_other0.668
r_chiral_restr0.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.337
r_dihedral_angle_4_deg16.845
r_dihedral_angle_3_deg11.345
r_dihedral_angle_1_deg7.445
r_angle_refined_deg1.795
r_mcangle_it0.96
r_angle_other_deg0.916
r_mcbond_it0.668
r_mcbond_other0.668
r_chiral_restr0.125
r_bond_refined_d0.019
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 Atoms746
Heterogen Atoms98

Software

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