3AU6

DNA polymerase X from Thermus thermophilus HB8 ternary complex with primer/template DNA and ddGTP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	50mM Tris-HCl (pH 8.5), 25mM MgSO4 7H2O, 1.8M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.166	α = 90
b = 80.166	β = 90
c = 268.555	γ = 90

Symmetry
Space Group	P 43 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	93	CCD	MARMOSAIC 225 mm CCD		2009-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1	SPring-8	BL26B2

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	3.3	76.82	99.3	0.065	14.8	11.5		13997

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	3.42	98.1		0.2		7.7	1326

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	3.3	50	13885	685	98.87	0.2589	0.2557	0.3194	RANDOM	83.2971

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]
3.96			3.96		-7.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.654
r_dihedral_angle_3_deg	21.936
r_dihedral_angle_4_deg	16.266
r_dihedral_angle_1_deg	7.452
r_scangle_it	1.876
r_angle_refined_deg	1.631
r_scbond_it	1.067
r_mcangle_it	0.997
r_angle_other_deg	0.944
r_mcbond_it	0.531

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.654
r_dihedral_angle_3_deg	21.936
r_dihedral_angle_4_deg	16.266
r_dihedral_angle_1_deg	7.452
r_scangle_it	1.876
r_angle_refined_deg	1.631
r_scbond_it	1.067
r_mcangle_it	0.997
r_angle_other_deg	0.944
r_mcbond_it	0.531
r_chiral_restr	0.075
r_mcbond_other	0.062
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4425
Nucleic Acid Atoms	346
Solvent Atoms	26
Heterogen Atoms	42

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

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.