1R9W | pdb_00001r9w

Crystal Structure of the DNA-binding domain of the human papillomavirus type 18 (HPV-18) replication initiation protein E1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F08	PDB entry 1F08 with non-identical residues mutated to alanines, and no solvent

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	290	PEG 4000, ammonium acetate, sodium citrate, DTT, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.54	α = 90
b = 46.24	β = 94.01
c = 43.19	γ = 90

Symmetry
Space Group	C 1 2 1

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		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.1	NSLS	X26C

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	1.8	30	93.3	0.049	17.5	3.41		12094		-3	12.7

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)
	1.8	1.91	69.1		0.135	5.7	2.25	1412

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1F08 with non-identical residues mutated to alanines, and no solvent	1.8	30	12094	11495	599	93	0.213	0.21	0.222	0.23	random	19.4

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.3
c_angle_d	1.5
c_improper_angle_d	1.01
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1104
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction

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.