2G7F

The 1.95 A crystal structure of Vibrio cholerae extracellular endonuclease I

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OUO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	293	30% PEG 8000 w/v, 0.2 M Na acetate, 0.1 M cacodylate buffer, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.4	α = 90
b = 64.75	β = 90
c = 75.78	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	120	IMAGE PLATE	RIGAKU RAXIS IV		2005-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.95	35.646	88.8	0.075	0.075	9.2	3.1	15108	13324	2	2	18.03

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.95	2.06	49	49	0.378	0.378	2	2	1019

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ouo	1.95	35.65	12666	13324	658	88.21	0.179	0.179	0.177	0.233	RANDOM	14.235

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]
-0.06			-0.07		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.428
r_dihedral_angle_4_deg	15.244
r_dihedral_angle_3_deg	14.002
r_dihedral_angle_1_deg	6.2
r_scangle_it	3.459
r_scbond_it	2.185
r_angle_refined_deg	1.446
r_mcangle_it	1.335
r_mcbond_it	0.793
r_nbtor_refined	0.293

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.428
r_dihedral_angle_4_deg	15.244
r_dihedral_angle_3_deg	14.002
r_dihedral_angle_1_deg	6.2
r_scangle_it	3.459
r_scbond_it	2.185
r_angle_refined_deg	1.446
r_mcangle_it	1.335
r_mcbond_it	0.793
r_nbtor_refined	0.293
r_symmetry_vdw_refined	0.208
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.101
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1702
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

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 R01GM133198.