7DKN | pdb_00007dkn

Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase

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	0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.072	α = 90
b = 52.705	β = 90
c = 61.618	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 4M		2018-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.1	Photon Factory	BL-1A

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	1.79	40.052	99.3	0.055	0.06	0.024	0.998	20.8	5.9		15203

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	1.79	1.83	92.4		0.141	0.166	0.085	0.973		3.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1wrj	1.79	40.052	15164	726	99.079	0.182	0.1802	0.19	0.2192	0.22	17.74

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]
0.01			-0.018		0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.684
r_dihedral_angle_4_deg	16.079
r_dihedral_angle_3_deg	12.998
r_dihedral_angle_1_deg	6.383
r_lrange_it	5.339
r_lrange_other	5.301
r_scangle_it	3.675
r_scangle_other	3.601
r_mcangle_it	2.356
r_mcangle_other	2.355
r_scbond_it	2.346
r_scbond_other	2.272
r_angle_refined_deg	1.689
r_mcbond_it	1.632
r_mcbond_other	1.583
r_angle_other_deg	1.414
r_symmetry_xyhbond_nbd_refined	0.4
r_nbd_refined	0.209
r_nbd_other	0.191
r_nbtor_refined	0.181
r_symmetry_nbd_other	0.17
r_xyhbond_nbd_refined	0.155
r_symmetry_nbd_refined	0.127
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1207
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	10

Software

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