8S5A | pdb_00008s5a

The crystal structure of FAN1 Nuclease bound to 5' phosphorylated p(dG)/3'(dT-dT-dT-dT) double flap DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RI8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.1 M Hepes/MOPS pH: 7.25, 0.1M Sodium formate 0.1M Ammonium acetate 0.1M Sodium citrate tribasic dihydrate 0.1M Potassium sodium tartrate tetrahydrate 0.1M Sodium oxamate 21% v/v Ethylene glycol 21 % w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.626	α = 90
b = 100.547	β = 90
c = 112.879	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 9M		2023-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9537	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.645	43.395	99.9	0.071	0.999	16.6	11.2		31091

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.645	2.691			0.845

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.645	43.395	31090	823	99.849	0.235	0.2343	0.2357	0.2731	0.2665	84.729

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]
-6.12			8.218		-2.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.263
r_dihedral_angle_4_deg	16.367
r_dihedral_angle_3_deg	13.919
r_lrange_it	7.983
r_lrange_other	7.981
r_dihedral_angle_1_deg	6.179
r_mcangle_it	5.821
r_mcangle_other	5.82
r_scangle_it	5.435
r_scangle_other	5.435
r_mcbond_it	3.767
r_mcbond_other	3.757
r_scbond_it	3.447
r_scbond_other	3.447
r_angle_refined_deg	1.249
r_angle_other_deg	1.179
r_nbd_other	0.161
r_nbd_refined	0.159
r_nbtor_refined	0.159
r_symmetry_nbd_other	0.151
r_xyhbond_nbd_refined	0.107
r_symmetry_xyhbond_nbd_refined	0.083
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.055
r_symmetry_nbd_refined	0.031
r_xyhbond_nbd_other	0.02
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_symmetry_xyhbond_nbd_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4785
Nucleic Acid Atoms	816
Solvent Atoms	16
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing