2W8L

Y-family DNA polymerase Dpo4 bypassing N2-naphthyl-guanine adduct in anti orientation

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4		DPO4:DNA COMPLEX (1:1.2 MOLAR RATIO, 150 MICROMOLAR), 20 MM TRIS HCL (PH 7.4), 15% POLYETHYLENE GLYCOL 3350 (W/V), 60 MM SODIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 4% GLYCEROL, 1 MM DGTP.

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.919	α = 90
b = 103.832	β = 90
c = 52.493	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARRESEARCH	MIRRORS	2008-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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	42.11	99.6	0.08	23.37	6.6		11751			57.3

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	3.19	100		0.77	4.7	7.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2BQR	3	29.25	10584	560	98.5	0.226	0.226	0.282	RANDOM	77.4

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]
5.56			-1.48		-4.09

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.2
c_scangle_it	3.5
c_mcangle_it	2.61
c_scbond_it	2.25
c_improper_angle_d	1.77
c_angle_deg	1.6
c_mcbond_it	1.5
c_bond_d	0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2754
Nucleic Acid Atoms	618
Solvent Atoms	43
Heterogen Atoms	34

Software

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