4QCB

Protein-DNA complex of Vaccinia virus D4 with double-stranded non-specific DNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52932:1 protein solution/reservoir (16% PEG6000, 0.08 M Tris, pH 8.5, 20% glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2445.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.389α = 90
b = 92.327β = 90
c = 142.859γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMirrors2014-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.8956.597.90.1580.1586.13122981199129.4
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)
12.893.0599.30.5050.5052.33

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 4DOF, CHAIN A2.8956.5176471138957797.280.218260.215750.2652RANDOM31.4
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]
0.030.08-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.522
r_dihedral_angle_4_deg13.994
r_dihedral_angle_3_deg13.732
r_long_range_B_refined6.804
r_long_range_B_other6.796
r_dihedral_angle_1_deg6.114
r_scangle_other3.981
r_mcangle_other2.838
r_scbond_other2.378
r_mcangle_it1.861
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.522
r_dihedral_angle_4_deg13.994
r_dihedral_angle_3_deg13.732
r_long_range_B_refined6.804
r_long_range_B_other6.796
r_dihedral_angle_1_deg6.114
r_scangle_other3.981
r_mcangle_other2.838
r_scbond_other2.378
r_mcangle_it1.861
r_scbond_it1.781
r_angle_other_deg1.297
r_angle_refined_deg1.185
r_mcbond_it1.07
r_mcbond_other1.07
r_chiral_restr0.07
r_bond_refined_d0.007
r_bond_other_d0.005
r_gen_planes_refined0.005
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 Atoms3432
Nucleic Acid Atoms445
Solvent Atoms118
Heterogen Atoms24

Software

Software
Software NamePurpose
RAPDdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling