X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP287Purified RNA was incubated at room temperature for 30 minutes in 25 mM Tris-HCl, pH 8.0, 50 mM potassium chloride, 10 mM magnesium chloride, 0.5 mM adenosylcobalamin prior to crystallization in 50 mM sodium cacodylate, 15% (v/v) PEG 400, 0.2 mM cobalt hexamine, 80 mM magnesium acetate, 1 mM spermine between pH 6.0 to pH 6.5 at 14C by vapor diffusion in a hanging drop format
Crystal Properties
Matthews coefficientSolvent content
5.5177.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.282α = 90
b = 118.282β = 90
c = 261.547γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-225Mirrors2013-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
13.25339.21392.80.160.1620.0250.99618.24715338
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.283.4643.84.1294.1680.5610.59854

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMIRASFREE R-VALUE3.2539.211533878586.30.2630.279129.1
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]
0.6930.3470.693-2.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.013
r_scangle_other3.118
r_scangle_it3.117
r_angle_other_deg2.165
r_scbond_it1.847
r_scbond_other1.847
r_dihedral_angle_3_deg1.736
r_angle_refined_deg0.807
r_nbtor_refined0.253
r_nbd_other0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.013
r_scangle_other3.118
r_scangle_it3.117
r_angle_other_deg2.165
r_scbond_it1.847
r_scbond_other1.847
r_dihedral_angle_3_deg1.736
r_angle_refined_deg0.807
r_nbtor_refined0.253
r_nbd_other0.22
r_xyhbond_nbd_refined0.208
r_nbd_refined0.148
r_chiral_restr0.074
r_gen_planes_refined0.033
r_gen_planes_other0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms3174
Solvent Atoms48
Heterogen Atoms179

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing
Cootmodel building