2P14

Crystal structure of small subunit (R.BspD6I2) of the heterodimeric restriction endonuclease R.BspD6I

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	298	2.0 M (NH4)2SO4, 0.2 M Li2SO4, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.429	α = 90
b = 38.36	β = 101.47
c = 61.995	γ = 90

Symmetry
Space Group	P 1 21 1

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	MAR CCD 165 mm	AU-COATED PLANAR and TOROIDAL MIRRORS	2006-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

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	1.5	20	99.3	0.054	21.2	2.91	29298	28430		2	18.66

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	1.5	1.53			0.47	2.24	2.87	1428

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ewf	1.5	10.75	28355	1428	99.37	0.179	0.177	0.211	RANDOM	18.891

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]
0.33		-0.36	-0.89		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.515
r_dihedral_angle_4_deg	15.856
r_dihedral_angle_3_deg	14.078
r_dihedral_angle_1_deg	4.694
r_scangle_it	4.003
r_scbond_it	2.579
r_mcangle_it	1.541
r_angle_refined_deg	1.421
r_mcbond_it	0.986
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.515
r_dihedral_angle_4_deg	15.856
r_dihedral_angle_3_deg	14.078
r_dihedral_angle_1_deg	4.694
r_scangle_it	4.003
r_scbond_it	2.579
r_mcangle_it	1.541
r_angle_refined_deg	1.421
r_mcbond_it	0.986
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.262
r_symmetry_vdw_refined	0.209
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1533
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Best	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.