2PU3 | pdb_00002pu3

Structural adaptation of endonuclease I from the cold-adapted and halophilic bacterium Vibrio salmonicida

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	298	30 % PEG 3350, 0.1 M Tris, 0.25 M sodium acetate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.078	α = 90
b = 44.948	β = 92.66
c = 51.746	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	ADSC QUANTUM 210		2005-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.0707	ESRF	ID29

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	1.5	33.923	99.3	0.047	0.047	9.4	4	31040	30823		2	10.24

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	1.5	1.58	97.6		0.074	0.074	14	3.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1OUO	1.5	33.92	31040	30823	1549	99.3	0.167	0.167	0.166	0.16	0.185	0.18	RANDOM	10.917

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]
-0.11		-0.04	-0.11		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.534
r_dihedral_angle_4_deg	14.561
r_dihedral_angle_3_deg	10.953
r_dihedral_angle_1_deg	5.771
r_scangle_it	2.897
r_scbond_it	1.797
r_mcangle_it	1.207
r_angle_refined_deg	1.142
r_mcbond_it	0.75
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.534
r_dihedral_angle_4_deg	14.561
r_dihedral_angle_3_deg	10.953
r_dihedral_angle_1_deg	5.771
r_scangle_it	2.897
r_scbond_it	1.797
r_mcangle_it	1.207
r_angle_refined_deg	1.142
r_mcbond_it	0.75
r_nbtor_refined	0.305
r_nbd_refined	0.19
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.093
r_symmetry_hbond_refined	0.083
r_chiral_restr	0.082
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1704
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	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.