2VA2 | pdb_00002va2

Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BQ3	PDB ENTRY 2BQ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4		30 MM NACL, 2%GLYCEROL, 10 MM TRIS PH 7.5, 2.5 MM CACL2, 0.5 MM DDCTP, 6% PEG 3350,0.1 MM AMMONIUM ACETATE, 0.05 CALCIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.139	α = 90
b = 101.875	β = 94.92
c = 111.062	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	2007-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B		APS	5ID-B

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	2.8	22.57	99.7	0.07	16.3	4.1		27671		1	41.1

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	2.8	2.9	99.8		0.4	3.42	4.2

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 2BQ3	2.8	22.57	28485	1383	99.7	0.211	0.211	0.2	0.25	0.25	RANDOM	51.4

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]
-12.07		0.29	15.95		-3.87

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.4
c_scangle_it	2.83
c_mcangle_it	2.27
c_scbond_it	1.75
c_mcbond_it	1.3
c_angle_deg	1.1
c_improper_angle_d	0.96
c_bond_d	0.007
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	5516
Nucleic Acid Atoms	1222
Solvent Atoms	217
Heterogen Atoms	60

Software

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