3IJM | pdb_00003ijm

The structure of a restriction endonuclease-like fold superfamily protein from Spirosoma linguale.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	279	0.1M NaCl, 0.1M Bis Tris pH6.5, 1.5M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 279K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.77	α = 90
b = 65.849	β = 90
c = 68.917	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	ADSC QUANTUM 210r		2009-07-31	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97950, 0.97992	APS	19-BM

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	1.7	50	99.9	0.058	10.1	7.2	33607	33607		-3	24.2

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	1.7	1.73	100		0.477		6.6	1674

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.7	29.42	33552	33552	1701	99.91	0.168	0.168	0.166	0.1736	0.199	0.2037	RANDOM	22.025

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]
-1.23			-2.24		3.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.469
r_dihedral_angle_4_deg	22.964
r_dihedral_angle_3_deg	11.925
r_dihedral_angle_1_deg	5.762
r_scangle_it	3.404
r_scbond_it	2.088
r_mcangle_it	1.454
r_angle_refined_deg	1.382
r_angle_other_deg	0.898
r_mcbond_it	0.862

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.469
r_dihedral_angle_4_deg	22.964
r_dihedral_angle_3_deg	11.925
r_dihedral_angle_1_deg	5.762
r_scangle_it	3.404
r_scbond_it	2.088
r_mcangle_it	1.454
r_angle_refined_deg	1.382
r_angle_other_deg	0.898
r_mcbond_it	0.862
r_mcbond_other	0.261
r_chiral_restr	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2298
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	18

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.