5LYE

Re-refined structure of the bacteriophage T4 short tail fibre PDB entry 1H6W containing 71 additionally identified residues


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629315-25 % (V/V) 2-METHYLPROPANE-2-OL (TERTIARY BUTANOL), 100 MM SODIUM CITRATE PH 5.6 10% (V/V) GLYCEROL, 10 MM HEPES, 150 MM SODIUM CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.257α = 90
b = 51.257β = 90
c = 249.491γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42000-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.919.892.30.0578.57.32868216.12
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)
11.9268.70.1544.85.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSIRASTHROUGHOUT1.919.827229145291.520.184730.183170.21465RANDOM37.983
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]
0.170.080.17-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.537
r_dihedral_angle_4_deg14.032
r_dihedral_angle_3_deg13.033
r_dihedral_angle_1_deg7.91
r_long_range_B_refined6.863
r_long_range_B_other6.578
r_scangle_other4.316
r_mcangle_it4.211
r_mcangle_other4.21
r_mcbond_it2.785
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.537
r_dihedral_angle_4_deg14.032
r_dihedral_angle_3_deg13.033
r_dihedral_angle_1_deg7.91
r_long_range_B_refined6.863
r_long_range_B_other6.578
r_scangle_other4.316
r_mcangle_it4.211
r_mcangle_other4.21
r_mcbond_it2.785
r_mcbond_other2.785
r_scbond_it2.701
r_scbond_other2.69
r_angle_refined_deg1.603
r_angle_other_deg1
r_chiral_restr0.104
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1734
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms7

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMACrefinement