7CSM | pdb_00007csm

Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase C120S variant

X-RAY DIFFRACTION

---

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
2.2	44.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.213	α = 90
b = 52.868	β = 90
c = 62.088	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		2019-06-29	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	1.25	48.21	99.1	0.038	0.042	0.016	0.999	27	6.5		44164

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	1.25	1.27	97.9		0.18	0.195	0.075	0.984		6.5

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	1.25	38.109	44110	2184	98.879	0.17	0.1688	0.17	0.1924	0.19	13.221

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]
0.002					-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.768
r_dihedral_angle_4_deg	16.873
r_dihedral_angle_3_deg	12.523
r_lrange_other	7.902
r_lrange_it	7.865
r_dihedral_angle_1_deg	6.711
r_scangle_other	3.354
r_scangle_it	3.346
r_scbond_it	2.295
r_scbond_other	2.27
r_angle_refined_deg	2.095
r_mcangle_it	1.834
r_mcangle_other	1.833
r_angle_other_deg	1.538
r_mcbond_it	1.336
r_mcbond_other	1.328
r_symmetry_xyhbond_nbd_refined	0.461
r_xyhbond_nbd_refined	0.341
r_nbd_refined	0.247
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.191
r_nbd_other	0.184
r_symmetry_nbd_refined	0.171
r_chiral_restr	0.125
r_symmetry_nbtor_other	0.09
r_symmetry_xyhbond_nbd_other	0.085
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1243
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	5

Software

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