5YTD | pdb_00005ytd

large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the natural base pair 5fC:dGTP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DFK

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
2.23	44.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.909	α = 90
b = 108.909	β = 90
c = 90.539	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		2014-09-03	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	94.32	99.8	23.68	7.2		40252

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	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4DFK	2	94.32	40252	2137	99.8	0.19822	0.19608	0.2	0.2387	0.23	RANDOM	52.76

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]
0.98	0.49		0.98		-3.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.003
r_dihedral_angle_4_deg	17.598
r_dihedral_angle_3_deg	14.235
r_dihedral_angle_1_deg	8.951
r_long_range_B_refined	4.572
r_long_range_B_other	4.438
r_scangle_other	1.79
r_mcangle_it	1.574
r_mcangle_other	1.574
r_angle_refined_deg	1.348
r_angle_other_deg	1.099
r_scbond_other	1.064
r_scbond_it	1.063
r_mcbond_it	0.982
r_mcbond_other	0.981
r_chiral_restr	0.082
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.003
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	4286
Nucleic Acid Atoms	569
Solvent Atoms	239
Heterogen Atoms	33

Software

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