Experiment: 2Q2U

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Structure of Chlorella virus DNA ligase bound to nicked DNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	A mixture of ChVLig (230 microM), nicked duplex DNA (220 microM) and 2 mM EDTA was added to an equal volume of a well solution containing 100 mM Bis-Tris-HCl (pH 6.5), 30 mM ammonium acetate, 22% PEG-4000. Crystals were grown at 22 C by the sitting-drop vapor diffusion method. Crystals appeared after 3 days. Crystals of ChVLig in complex with nicked DNA were transferred to a solution containing 100 mM Bis-Tris-HCl (pH 6.5), 110 mM ammonium acetate, 22.5% PEG-4000, 5 mM MnCl2 for 5 min, then placed into a solution containing the same components plus 15% glycerol prior to flash-freezing the crystals in liquid nitrogen., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.475	α = 70.32
b = 92.895	β = 78.45
c = 89.633	γ = 89.87

Symmetry
Space Group	P 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	MAR CCD 165 mm	Double crystal monochromator. Si(111) or Si(220) options. Sagitall focusing. Cylindrically bent ULE mirror with Pt and Rh coating.	2006-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9A	0.9795	NSLS	X9A

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	3	50	95.8	0.078	7.3	1.9	41596	39849		-1

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)
	3	3.11	87.7		0.455	1.4	1.7	3651

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Structure of Chlorella virus DNA ligase bound to nicked DNA	3	24.88	39420	38001	1924	96.4	0.249	0.24	0.283	0.23	RANDOM	46.4

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]
-7.99	0.07	-2.18		-5.11	7.99

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.8
c_scangle_it	2.86
c_mcangle_it	1.9
c_scbond_it	1.69
c_angle_deg	1.1
c_mcbond_it	1.07
c_improper_angle_d	1.06
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9440
Nucleic Acid Atoms	3428
Solvent Atoms	56
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
AMoRE	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.