7UI4

Crystal structure of the DNA preQ0 insertase DpdA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	mixing 2 ul sample containing 4.0 mg/ml protein (81.5 uM), 0.5 mM guanine, 50 mM Tris (pH 7.5), 100 mM NaCl and 1 mM DTT with 3 ul reservoir solution containing 10% (w/v) polyethylene glycol (PEG) 8000, 8% (v/v) ethylene glycol (EG), 100 mM HEPES (pH 7.5), 0.1 mM ZnCl2, 3 mM reduced glutathione (GSH) and 3 mM oxidized glutathione (GSSG)

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.102	α = 90
b = 141.768	β = 90
c = 42.496	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARMOSAIC 325 mm CCD		2017-06-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1.28149, 0.98397, 1.28268	SSRL	BL14-1

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	2.51	73.59	87.1	0.103	0.107	0.029	0.999	21.8	12.8		16179

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	2.51	2.65	50.4		0.964	1.025	0.341	0.92		8.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.51	54.78	15348	790	87.09	0.1322	0.1298	0.1785	RANDOM	55.874

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]
-1.43			1.96		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	44.532
r_dihedral_angle_2_deg	35.327
r_sphericity_bonded	30.176
r_dihedral_angle_4_deg	21.219
r_dihedral_angle_3_deg	19.215
r_dihedral_angle_1_deg	6.617
r_rigid_bond_restr	2.082
r_angle_refined_deg	1.078
r_angle_other_deg	0.847
r_chiral_restr	0.054
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3367
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing