5MDN

Structure of the family B DNA polymerase from the hyperthermophilic archaeon Pyrobaculum calidifontis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XHB	2xhb, 3a2f, 1wn7, 1s5j
experimental model	PDB	3A2F	2xhb, 3a2f, 1wn7, 1s5j
experimental model	PDB	1WN7	2xhb, 3a2f, 1wn7, 1s5j
experimental model	PDB	1S5J	2xhb, 3a2f, 1wn7, 1s5j

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	294	PEG 3350, potassium thiocyanate, Bis-Tris propane

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.19	α = 90
b = 100.742	β = 94.72
c = 119.335	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	100	PIXEL	DECTRIS PILATUS 6M-F		2016-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	118.93	97.5	0.1	0.99	6.8	3.6		42313

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	96.9		0.77	0.59	1.8	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2xhb, 3a2f, 1wn7, 1s5j	2.8	65.247	1.34	41959	2132	96.93	0.2537	0.2517	0.2896

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.925
f_angle_d	0.733
f_chiral_restr	0.048
f_plane_restr	0.005
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12260
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHENIX	refinement
MOLREP	phasing
Aimless	data scaling
DIALS	data reduction

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 R01GM133198.