3LDY

An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	20-24% PEG 3000, 2-5% ethylene glycol, 0.1M sodium citrate., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.908	α = 90
b = 115.788	β = 90
c = 114.689	γ = 90

Symmetry
Space Group	C 2 2 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 210	mirrors	2009-10-31	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU SATURN 944		2009-01-01	M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD	ADSC QUANTUM 315	mirrors	2009-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1
2	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418
3	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0719	ALS	5.0.2

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
1,2,3	1.83	50	87.9	0.066	26	9.8		19597		2	26.25

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)
1,2,3	1.83	1.9	39.2		0.25	2.26	2.7	2194

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	MIR	THROUGHOUT	1.97	28.95	3	19083	16445	888	96.99	0.186	0.186	0.1843	0.21725	RANDOM	41.047

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]
0.04			3.35		-3.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.365
r_dihedral_angle_4_deg	21.948
r_dihedral_angle_3_deg	16.333
r_dihedral_angle_1_deg	6.338
r_scangle_it	4.493
r_scbond_it	2.99
r_mcangle_it	2.139
r_rigid_bond_restr	1.674
r_angle_refined_deg	1.542
r_mcbond_it	1.163

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.365
r_dihedral_angle_4_deg	21.948
r_dihedral_angle_3_deg	16.333
r_dihedral_angle_1_deg	6.338
r_scangle_it	4.493
r_scbond_it	2.99
r_mcangle_it	2.139
r_rigid_bond_restr	1.674
r_angle_refined_deg	1.542
r_mcbond_it	1.163
r_chiral_restr	0.098
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1102
Nucleic Acid Atoms	366
Solvent Atoms	89
Heterogen Atoms	3

Software

Software
Software Name	Purpose
ADSC	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

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.