1VP7

Crystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella pertussis at 2.40 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	7.5	277	2.0M (NH4)2SO4, 2.0% PEG-400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.75	66.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.03	α = 90
b = 107.03	β = 90
c = 207.26	γ = 120

Symmetry
Space Group	P 6 2 2

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		2004-09-18	M	SINGLE WAVELENGTH
2	1	x-ray		M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1
2	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.979694,0.979811,1.020035	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.4	29.02	99.9	0.13	18	11.7		28264			42.73

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.4	2.53	100		0.616	3.6	6.8	4033

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	2.4	29.02	26875	1388	99.88	0.20473	0.20268	0.2444	RANDOM	32.774

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]
1.31	0.66		1.31		-1.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.728
r_dihedral_angle_4_deg	17.055
r_dihedral_angle_3_deg	16.045
r_scangle_it	11.232
r_scbond_it	7.925
r_dihedral_angle_1_deg	4.946
r_mcangle_it	3.852
r_mcbond_it	2.903
r_angle_refined_deg	1.605
r_nbtor_refined	0.293

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.728
r_dihedral_angle_4_deg	17.055
r_dihedral_angle_3_deg	16.045
r_scangle_it	11.232
r_scbond_it	7.925
r_dihedral_angle_1_deg	4.946
r_mcangle_it	3.852
r_mcbond_it	2.903
r_angle_refined_deg	1.605
r_nbtor_refined	0.293
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.204
r_xyhbond_nbd_refined	0.12
r_symmetry_hbond_refined	0.113
r_chiral_restr	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3129
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELX	model building
autoSHARP	phasing
REFMAC	refinement
CCP4	data scaling
SHELX	phasing

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.