2C2D | pdb_00002c2d

Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C28	PDB ENTRY 2C28

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		5% PEG 3350, 10 MM TRIS-HCL PH 7.5, 50 MM CA(CH3CO2)2, 30MM NACL, 1.25% GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.507	α = 90
b = 102.017	β = 90
c = 53.093	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	ADSC CCD		2005-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1

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	2.56	43.99	97	0.09	16.48	9.78		17022		1	80.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.56	2.72	81.7

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 (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 2C28	2.57	43.99	17021	828	97	0.24	0.24	0.23	0.28	0.27	RANDOM	78.6

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]
6.42			-3.25		-3.17

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.2
c_mcangle_it	2.94
c_scangle_it	2.85
c_angle_deg	1.9
c_scbond_it	1.72
c_mcbond_it	1.64
c_improper_angle_d	1.22
c_bond_d	0.011
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	2744
Nucleic Acid Atoms	569
Solvent Atoms	96
Heterogen Atoms	65

Software

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