4YIG | pdb_00004yig

vaccinia virus D4/A20(1-50) in complex with dsDNA containing an abasic site and free uracyl

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OD8	4OD8,1SSP
experimental model	PDB	1SSP	4OD8,1SSP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	293	0.2M ammonium chloride, 10% W/V PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.092	α = 90
b = 136.092	β = 90
c = 161.073	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9763	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.7	48.86	99.9	0.045	19.1	5		46345

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.79	100		0.492	2.9	5.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4OD8,1SSP	2.7	48.86	44109	2227	99.87	0.18227	0.17993	0.19	0.22764	0.23	RANDOM	73.761

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]
0.29	0.14		0.29		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.468
r_dihedral_angle_3_deg	18.443
r_dihedral_angle_4_deg	17.286
r_long_range_B_refined	12.004
r_long_range_B_other	12.004
r_scangle_other	9.702
r_mcangle_it	8.302
r_mcangle_other	8.301
r_dihedral_angle_1_deg	7.456
r_scbond_it	6.81
r_scbond_other	6.809
r_mcbond_it	5.943
r_mcbond_other	5.943
r_angle_refined_deg	1.82
r_angle_other_deg	1.348
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	6558
Nucleic Acid Atoms	1188
Solvent Atoms	54
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing