7DQQ

Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase Y91F/C120S variant in complex with O6-methyldeoxyguanosine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WRJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	5% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.0, 10% w/v Polyethylene glycol monomethyl ether 5,000

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.473	α = 90
b = 53.166	β = 90
c = 62.085	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 PILATUS3 S 6M		2018-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.00	Photon Factory	BL-5A

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	2.6	48.47	100	0.04	0.044	0.017	0.999	32.3	6.3		5304

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	2.6	2.72	100		0.139	0.151	0.059	0.99		6.6

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	1wrj	2.6	38.236	5274	265	99.943	0.196	0.1911	0.2841	27.542

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]
-0.003			0.042		-0.039

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.008
r_dihedral_angle_4_deg	20.534
r_dihedral_angle_3_deg	18.216
r_dihedral_angle_1_deg	6.684
r_lrange_it	6.339
r_lrange_other	6.333
r_scangle_it	3.779
r_scangle_other	3.777
r_mcangle_it	3.354
r_mcangle_other	3.353
r_scbond_it	2.262
r_scbond_other	2.26
r_mcbond_it	2.007
r_mcbond_other	2.003
r_angle_refined_deg	1.571
r_angle_other_deg	1.213
r_nbd_other	0.211
r_nbd_refined	0.201
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.17
r_symmetry_nbd_refined	0.159
r_xyhbond_nbd_refined	0.141
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1195
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	20

Software

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