X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 295.0
Details EcoLigA (0.3 mM) was reacted with 5 mM MgCl2 and 0.3 mM NAD+ for 30 min at 22 C. The ligase-adenylylation reaction was then quenched by adding 10 mM EDTA. The mixture was supplemented with 26-bp nicked duplex DNA (0.318 mM). This LigA-nucleic acid solution was mixed 1:2 with a well solution containing 200 mM ammonium sulfate, 50 mM sodium acetate, 24% PEG-4000. Crystals were grown at 22 C by the sitting drop vapor diffusion method. Crystals appeared after 3 days. The crystals were transferred serially to solutions containing 5% glycerol/24% PEG-4000, 10% glycerol/26% PEG-4000, 15% glycerol/28% PEG-4000, and 20% glycerol/30% PEG-4000 in 100 mM ammonium sulfate, 50 mM sodium acetate, after which they were flash-frozen in liquid nitrogen. , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.44 α = 90
b = 99.27 β = 105.33
c = 86.25 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2006-12-19
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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
2.3 40 98.7 0.084 -- -- 4.0 39615 39100 -3.0 -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.3 2.38 91.2 0.422 -- -- 3.5 3598

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.3 30.34 -- 0.0 39734 39098 1959 98.4 -- -- 0.217 0.254 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.3 2.44 5876 303 5573 0.286 0.321 0.018 88.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 39.4
Anisotropic B[1][1] -2.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.85
Anisotropic B[2][2] -0.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.2
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 2.05
c_scangle_it 3.06
c_angle_deg 1.2
c_mcangle_it 2.18
c_dihedral_angle_d 21.4
c_mcbond_it 1.34
c_bond_d 0.006
c_improper_angle_d 1.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.3
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.35
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4565
Nucleic Acid Atoms 1062
Heterogen Atoms 44
Solvent Atoms 320

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement version: 1.1
PDB_EXTRACT data extraction version: 2.000
ADSC data collection version: QUANTUM
MOLREP phasing