5JKS | pdb_00005jks

vaccinia virus D4 R167A mutant /A20(1-50)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82930.1M bicine pH 7.8, 1.6M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.856.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.98α = 90
b = 92.98β = 90
c = 145.71γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray107PIXELDECTRIS PILATUS 6M2014-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.978ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.7928.8499.615.49.718696
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.792.9597.53.59.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4ODA2.7928.841772594099.560.178440.175550.180.23340.23RANDOM58.262
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.157
r_dihedral_angle_3_deg17.954
r_dihedral_angle_4_deg14.606
r_long_range_B_refined10.526
r_long_range_B_other10.526
r_scangle_other8.033
r_dihedral_angle_1_deg6.707
r_mcangle_it6.659
r_mcangle_other6.657
r_scbond_it5.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.157
r_dihedral_angle_3_deg17.954
r_dihedral_angle_4_deg14.606
r_long_range_B_refined10.526
r_long_range_B_other10.526
r_scangle_other8.033
r_dihedral_angle_1_deg6.707
r_mcangle_it6.659
r_mcangle_other6.657
r_scbond_it5.216
r_scbond_other5.086
r_mcbond_it4.436
r_mcbond_other4.435
r_angle_refined_deg1.826
r_angle_other_deg1.061
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 Atoms4323
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing