Experiment: 1TA8

Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B04	Ligase adenylation domain from Bacillus stearothermophilus (PDB ID: 1B04)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	286	Ammonium sulfate, cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 13K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.167	α = 90
b = 86.105	β = 100.99
c = 57.108	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	MARRESEARCH	Osmic Confocal Max-Flux Optics	2003-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.5418

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	1.8	25	99.95	0.051	16.5	3.7	39492	39373	1	1	21.2

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	1.8	1.86	99.5		0.456	2.7	3.4	3908

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	Ligase adenylation domain from Bacillus stearothermophilus (PDB ID: 1B04)	1.8	24.33	39473	38113	3817	96.2	0.203	0.203	0.2	0.1979	0.225	0.2223	RANDOM	27

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]
1.1		-0.73	5.2		-6.3

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.2
c_scangle_it	3.28
c_scbond_it	2.19
c_improper_angle_d	2.06
c_mcangle_it	1.9
c_mcbond_it	1.26
c_angle_deg	1.2
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2513
Nucleic Acid Atoms
Solvent Atoms	306
Heterogen Atoms	38

Software

Software
Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing