2P1J

Crystal structure of a polC-type DNA polymerase III exonuclease domain from Thermotoga maritima

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.6	294	100mM Tris-HCl pH 8.6, 20% Glycerol, 14% PEG 10000, 150mM Sodium chloride, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.703	α = 90
b = 124.939	β = 90
c = 143.062	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2007-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.5	24.05	96.4	0.106	0.106	14.9	7.2	17030	17030			69.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	91.5		0.816	0.816	1.5	7.2	2323

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.5	20	16961	16961	848	96.02	0.232	0.229	0.298	RANDOM	64.804

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]
3.53			1.75		-5.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.847
r_dihedral_angle_3_deg	23.851
r_dihedral_angle_4_deg	22.669
r_dihedral_angle_1_deg	9.273
r_scangle_it	3.621
r_scbond_it	2.306
r_angle_refined_deg	1.958
r_mcangle_it	1.808
r_mcbond_it	1.059
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.847
r_dihedral_angle_3_deg	23.851
r_dihedral_angle_4_deg	22.669
r_dihedral_angle_1_deg	9.273
r_scangle_it	3.621
r_scbond_it	2.306
r_angle_refined_deg	1.958
r_mcangle_it	1.808
r_mcbond_it	1.059
r_nbtor_refined	0.32
r_nbd_refined	0.267
r_symmetry_vdw_refined	0.222
r_symmetry_hbond_refined	0.218
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.144
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2723
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.