1S68

Structure and Mechanism of RNA Ligase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5296100mM Tris, 8.5, 0.2M sodium acetate, 5mM DTT, 28% PEG-3350, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.3447.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.717α = 90
b = 89.892β = 90
c = 47.737γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVosmic2003-05-15MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 4sag focus2003-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418
2SYNCHROTRONNSLS BEAMLINE X4A0.9790NSLSX4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1,21.95097.10.0618.21976623.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.92.0283.20.3222.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUT1.934.052022819459100096.20.190.190.227RANDOM29.1
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]
-3.036.06-3.03
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.4
c_scangle_it3.64
c_scbond_it2.54
c_mcangle_it2.09
c_mcbond_it1.32
c_angle_deg1.3
c_improper_angle_d0.74
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1865
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms23

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing