2OKC

Crystal structure of Type I restriction enzyme StySJI M protein (NP_813429.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.33	277	NANODROP, 7.5% 2-propanol, 20.0% polyethylene glycol 4000, 0.1M HEPES pH 7.33, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.44	α = 90
b = 85.85	β = 90
c = 152.81	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	CCD	MARMOSAIC 325 mm CCD	FLAT MIRROR (VERTICAL FOCUSING)	2006-12-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97899, 0.97935	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	28.62	88.9	0.049	11.63	3.97		46716			45.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	86.2		0.378	2.2

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	2.2	28.62	46612	2367	91.8	0.185	0.182	0.232	RANDOM	41.37

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]
0.04			-0.24		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.97
r_dihedral_angle_4_deg	17.107
r_dihedral_angle_3_deg	14.981
r_dihedral_angle_1_deg	7.312
r_scangle_it	6.304
r_scbond_it	4.888
r_mcangle_it	2.961
r_mcbond_it	1.938
r_angle_refined_deg	1.565
r_angle_other_deg	0.848
r_mcbond_other	0.454
r_nbd_refined	0.218
r_symmetry_vdw_other	0.195
r_nbd_other	0.183
r_nbtor_refined	0.181
r_symmetry_vdw_refined	0.181
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.14
r_chiral_restr	0.086
r_nbtor_other	0.085
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6629
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	69

Software

Software
Software Name	Purpose
MolProbity	model building
SOLVE	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction