5YTC

Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the unnatural base M-fC pair with dATP in the active site

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	8.5	293.15	0.2 M Mg(HCOO)2, 0.1 M Tris HCl (pH 8.5), 18% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.886	α = 90
b = 108.886	β = 90
c = 90.533	γ = 120

Symmetry
Space Group	P 31 2 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	CCD	MAR CCD 130 mm		2016-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.9793	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.28	94.3	98	19.27	5.1		25784

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	2.28	2.32

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4DFK	2.28	94.3	25784	1453	95.11	0.19742	0.19412	0.25762	RANDOM	38.653

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]
-0.29	-0.14		-0.29		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.86
r_dihedral_angle_4_deg	17.86
r_dihedral_angle_3_deg	16.619
r_dihedral_angle_1_deg	9.017
r_long_range_B_refined	2.671
r_long_range_B_other	2.524
r_angle_refined_deg	1.461
r_angle_other_deg	1.014
r_scangle_other	0.822
r_mcangle_it	0.782
r_mcangle_other	0.782
r_scbond_it	0.466
r_scbond_other	0.465
r_mcbond_it	0.435
r_mcbond_other	0.434
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4266
Nucleic Acid Atoms	573
Solvent Atoms	262
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing