7ON0

Thermus sp. 2.9 DarT in complex with ADP-ribosylated ssDNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OMV	D_1292116023

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	123 mM potassium thiocyanate, 12% (w/v) PEG2000MME

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.889	α = 90
b = 38.683	β = 101.756
c = 61.012	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		2019-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.8998	Diamond	I24

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	1.46	38.68	100	0.132	0.144	0.057	0.995	7.4	6.4		33508

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	1.46	1.49	99.9		1.307	1.452	0.623	0.513	1.1	5.3

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	D_1292116023	1.46	32.49	33491	1622	99.958	0.164	0.1622	0.1903	16.031

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]
-0.394		-0.398	0.377		0.169

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.305
r_dihedral_angle_4_deg	22.105
r_dihedral_angle_3_deg	13.038
r_dihedral_angle_1_deg	7.026
r_lrange_it	4.484
r_lrange_other	4.353
r_scangle_it	2.397
r_scangle_other	2.396
r_angle_refined_deg	1.909
r_scbond_it	1.592
r_scbond_other	1.591
r_angle_other_deg	1.477
r_mcangle_it	1.374
r_mcangle_other	1.374
r_mcbond_it	0.913
r_mcbond_other	0.912
r_symmetry_nbd_refined	0.324
r_symmetry_xyhbond_nbd_refined	0.242
r_nbd_refined	0.241
r_nbd_other	0.241
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1724
Nucleic Acid Atoms	98
Solvent Atoms	226
Heterogen Atoms	35

Software

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