3UQ8 | pdb_00003uq8

Structure of adenylation domain of Haemophilus influenzae DNA ligases bound to NAD+ in adenylated state.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		The reservoir solution contained 16% (w/v) polyethylene glycol (PEG) 3500 and 350 mM sodium potassium tartrate. Hanging drops were set up at 18 C by mixing 2 l of protein solution with 2 l of the reservoir solution and crystals were observed within 3-4 days. , pH 7.5, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.233	α = 90
b = 70.233	β = 90
c = 161.286	γ = 90

Symmetry
Space Group	P 43 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	298	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	32.2	90.69				41079	20	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	32.2	41079	2070	90.65	0.1868	0.1852	0.2162	0.2468	RANDOM	14.6855

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.212
r_dihedral_angle_4_deg	14.549
r_dihedral_angle_3_deg	12.088
r_dihedral_angle_1_deg	5.692
r_scangle_it	5.203
r_scbond_it	3.343
r_mcangle_it	2.06
r_angle_refined_deg	2.021
r_mcbond_it	1.222
r_chiral_restr	0.155
r_bond_refined_d	0.024
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2551
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	66

Software

Software
Software Name	Purpose
MOSFLM	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SCALA	data scaling
AMoRE	phasing