5Z3N | pdb_00005z3n

Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA

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, 24% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.947	α = 90
b = 107.947	β = 90
c = 90.121	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		2017-12-15	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	1.91	93.49	99.8	18.69	6.4		42010

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	1.91	1.94

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	1.91	93.48	42010	2215	92.94	0.18568	0.1834	0.19	0.22933	0.23	RANDOM	26.317

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]
-0.18	-0.09		-0.18		0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.163
r_dihedral_angle_4_deg	16.501
r_dihedral_angle_3_deg	14.297
r_dihedral_angle_1_deg	9.287
r_long_range_B_refined	5.794
r_long_range_B_other	5.794
r_angle_refined_deg	1.55
r_angle_other_deg	1.152
r_scangle_other	0.791
r_mcangle_it	0.707
r_mcangle_other	0.707
r_scbond_it	0.467
r_scbond_other	0.467
r_mcbond_it	0.396
r_mcbond_other	0.394
r_chiral_restr	0.091
r_bond_refined_d	0.01
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	4278
Nucleic Acid Atoms	568
Solvent Atoms	498
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing