4DYQ

High resolution crystal structure of terminase small subunit gp1 of the bacterial virus sf6


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.42931.2M NAH2PO4/0.8M K2HPO4, 0.2M Li2SO4, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
2.2946.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.705α = 90
b = 88.705β = 90
c = 72.394γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 315rRh coated flat mirror2009-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.97946SSRLBL7-1

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
11.55097.90.04450.1836.74660745628-319.318
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5597.60.5030.5032.86.44462

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3HEF1.50219.1254660743953192594.410.1780.17690.202Random19.318
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]
-2.938-2.9385.876
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.692
f_angle_d0.891
f_chiral_restr0.051
f_bond_d0.005
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1979
Nucleic Acid Atoms
Solvent Atoms264
Heterogen Atoms

Software

Software
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing