2AYB | pdb_00002ayb

Crystal structure of HPV6a E2 DNA Binding Domain bound to a 16 base pair DNA target

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R8H	Protein of PDB entry 1R8H DNA of PDB entry 1JJ4
experimental model	PDB	1JJ4	Protein of PDB entry 1R8H DNA of PDB entry 1JJ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	tri-Sodium citrate dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.6	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.247	α = 90
b = 75.247	β = 90
c = 97.426	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	BRUKER SMART 6000	mirrors	2005-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER X8 PROTEUM	1.548

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	3.2	65.23	99.37	0.138	19.8	22.5	5168	4928	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)
1	3.2	3.28	100		0.387	5.2	22.5	362

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Protein of PDB entry 1R8H DNA of PDB entry 1JJ4	3.2	65.23	4928	4928	240	99.37	0.194	0.259	0.189	0.19	0.297	0.29	RANDOM	41.3

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]
2.2	1.1		2.2		-3.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.318
r_dihedral_angle_3_deg	20.966
r_dihedral_angle_4_deg	19.688
r_dihedral_angle_1_deg	9.067
r_angle_refined_deg	2.148
r_scangle_it	1.742
r_scbond_it	1.021
r_mcangle_it	1.02
r_mcbond_it	0.552
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.318
r_dihedral_angle_3_deg	20.966
r_dihedral_angle_4_deg	19.688
r_dihedral_angle_1_deg	9.067
r_angle_refined_deg	2.148
r_scangle_it	1.742
r_scbond_it	1.021
r_mcangle_it	1.02
r_mcbond_it	0.552
r_nbtor_refined	0.32
r_nbd_refined	0.25
r_symmetry_hbond_refined	0.198
r_symmetry_vdw_refined	0.179
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.111
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1444
Nucleic Acid Atoms	650
Solvent Atoms	12
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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.