4GMA

Crystal structure of the adenosylcobalamin riboswitch


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop7.529810% isopropanol, 300 mM magnesium chloride, 100 mM sodium HEPES pH 7.5, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.169.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.648α = 90
b = 243.545β = 90
c = 87.102γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
21
31
41
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.20.97ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1,23.9488.37499.40.04813.73.58706
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,24.644.8999.90.4980.4981.63.6855

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUT3.9442.269479870641192.230.26220.26280.26220.2752RANDOM220.6988
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]
-5.762-23.21928.981
RMS Deviations
KeyRefinement Restraint Deviation
c_mcangle_it38.739
c_mcbond_it30.189
c_angle_d0.867
c_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms4140
Solvent Atoms
Heterogen Atoms109

Software

Software
Software NamePurpose
SCALAdata scaling
BUSTER-TNTrefinement
SHARPphasing
PDB_EXTRACTdata extraction
XDSdata reduction