5YTF

Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base M-fC pair with dA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7	293.15	0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.69	α = 90
b = 107.69	β = 90
c = 90.319	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		2016-12-25	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	1.98	93.26	100	11	5.3		40333

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	1.98	2.03

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	1.98	93.26	40333	2127	99.96	0.18336	0.18073	0.23256	RANDOM	34.465

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]
0.58	0.29		0.58		-1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.191
r_dihedral_angle_4_deg	18.856
r_dihedral_angle_3_deg	15.845
r_dihedral_angle_1_deg	10.238
r_long_range_B_refined	3.318
r_long_range_B_other	3.318
r_scangle_other	1.791
r_angle_refined_deg	1.768
r_mcangle_it	1.307
r_mcangle_other	1.307
r_angle_other_deg	1.219
r_scbond_it	1.108
r_scbond_other	1.108
r_mcbond_it	0.83
r_mcbond_other	0.827
r_chiral_restr	0.101
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
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	4278
Nucleic Acid Atoms	573
Solvent Atoms	358
Heterogen Atoms	39

Software

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