3GDE

The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	294	100mM Tris-HCl, pH9.0, 0.4M sodium dihydrogen phosphate, 1.2M dipotassium hydrogen phosphate, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.355	α = 90
b = 94.355	β = 90
c = 197.416	γ = 90

Symmetry
Space Group	P 41 21 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 QUANTUM 210		2006-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 4A	1.0000	PAL/PLS	4A

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	2.3	20	100	0.089	36			40500

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)
	2.3	2.38	100		0.44	5.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2CFM	2.3	20	36294	4007	99.84	0.221	0.215	0.277	RANDOM	37.035

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]
1.62			1.62		-3.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.166
r_dihedral_angle_4_deg	19.356
r_dihedral_angle_3_deg	18.92
r_dihedral_angle_1_deg	7.246
r_scangle_it	2.765
r_scbond_it	1.622
r_angle_refined_deg	1.314
r_mcangle_it	1.189
r_mcbond_it	0.683
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.187
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.098
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4423
Nucleic Acid Atoms
Solvent Atoms	458
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing