8XK7 | pdb_00008xk7

binary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		structure of apo SFM4-3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.2 M lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, and 28% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.61	α = 90
b = 65.628	β = 103.51
c = 107.378	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 PILATUS3 6M		2021-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.979	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	50	98.8	0.135	0.148	0.06	0.974	4.3	6.1		55909

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	99.7		0.586	0.64	0.255	0.915		6.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	24.41	53014	2832	98.77	0.19347	0.19151	0.2012	0.2311	0.2324	RANDOM	36.354

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]
1.66		-1.33	3.74		-4.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.286
r_dihedral_angle_2_deg	12.959
r_long_range_B_refined	5.957
r_long_range_B_other	5.957
r_dihedral_angle_1_deg	5.837
r_scangle_other	4.326
r_mcangle_other	3.294
r_mcangle_it	3.293
r_scbond_it	2.843
r_scbond_other	2.842
r_mcbond_it	2.282
r_mcbond_other	2.282
r_angle_refined_deg	1.363
r_angle_other_deg	0.386
r_chiral_restr	0.081
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	4315
Nucleic Acid Atoms	619
Solvent Atoms	346
Heterogen Atoms	32

Software

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