2W9B

Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ASD	PDB ENTRY 2ASD

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, 1 MM DGTP.

Crystal Properties
Matthews coefficient	Solvent content
2.42	53.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.794	α = 90
b = 101.776	β = 91.95
c = 97.268	γ = 90

Symmetry
Space Group	P 1 21 1

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	2008-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F		APS	21-ID-F

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	2.28	28.75	96.4	0.1	10.3	3.9		45625			41

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	2.28	2.42	89.7		0.26	3.8	6.8

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 2ASD	2.28	28.75	44372	2231	96.4	0.239	0.239	0.251	RANDOM	36.3

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]
1.38		2.31	-5.52		4.14

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.5
c_scangle_it	3.64
c_angle_deg	3.2
c_scbond_it	2.75
c_improper_angle_d	2.39
c_mcangle_it	2.27
c_mcbond_it	1.4
c_bond_d	0.034
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	5500
Nucleic Acid Atoms	1220
Solvent Atoms	203
Heterogen Atoms	4

Software

Software
Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing