2AYG

Crystal structure of HPV6a E2 DNA binding domain bound to an 18 base pair DNA target

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	sodium chloride, Hepes, ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.449	α = 90
b = 73.449	β = 90
c = 109.237	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4	mirrors	2005-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1	1.488	SRS	PX14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.1	63.63	99.9	0.118	17.9	7.6	5807	6087	2	2

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)
	3.1	3.18	99.8		0.351	4.2	7.1	429

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry 1JJ4	3.1	63.63	5807	6085	278	99.85	0.206	0.247	0.203	0.288	RANDOM	64.548

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]
4.17	2.08		4.17		-6.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.469
r_dihedral_angle_4_deg	22.469
r_dihedral_angle_3_deg	22.032
r_dihedral_angle_1_deg	12
r_angle_refined_deg	2.322
r_scangle_it	2.085
r_mcangle_it	1.376
r_scbond_it	1.203
r_mcbond_it	0.744
r_nbtor_refined	0.325

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.469
r_dihedral_angle_4_deg	22.469
r_dihedral_angle_3_deg	22.032
r_dihedral_angle_1_deg	12
r_angle_refined_deg	2.322
r_scangle_it	2.085
r_mcangle_it	1.376
r_scbond_it	1.203
r_mcbond_it	0.744
r_nbtor_refined	0.325
r_nbd_refined	0.278
r_chiral_restr	0.26
r_symmetry_vdw_refined	0.227
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.029
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1444
Nucleic Acid Atoms	732
Solvent Atoms	19
Heterogen Atoms

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.