7OMZ | pdb_00007omz

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

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	150 mM potassium thiocyanate, 10% (w/v) PEG2000MME

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.963	α = 90
b = 38.89	β = 101.805
c = 61.179	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	1.66	38.89	98.1	0.134	0.149	0.063	0.992	6.6	5.3		22671

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	1.66	1.69	80.7		0.622	0.721	0.356	0.722	1.6	3.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	D_1292116023	1.66	37.685	22657	1076	98.023	0.153	0.1512	0.16	0.1805	0.18	17.738

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]
-1.027		0.269	0.866		0.045

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.347
r_dihedral_angle_4_deg	23.795
r_dihedral_angle_3_deg	12.32
r_dihedral_angle_1_deg	7.275
r_lrange_it	4.859
r_lrange_other	4.638
r_scangle_it	2.732
r_scangle_other	2.731
r_angle_refined_deg	1.847
r_scbond_it	1.71
r_scbond_other	1.71
r_mcangle_it	1.585
r_mcangle_other	1.585
r_angle_other_deg	1.405
r_mcbond_it	1.055
r_mcbond_other	1.051
r_nbd_refined	0.236
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.168
r_nbd_other	0.167
r_symmetry_xyhbond_nbd_refined	0.161
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.083
r_symmetry_nbd_refined	0.066
r_gen_planes_refined	0.014
r_bond_refined_d	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	99
Solvent Atoms	202
Heterogen Atoms	47

Software

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