X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOtherA-form RNA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5292MgCl2, Li2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.2244.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.96α = 90
b = 38.85β = 89.98
c = 77.72γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.808EMBL/DESY, HAMBURGX13

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
11.232099.10.05821.37.1320553205514.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.231.2598.10.35.76.21502

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTA-RNA model1.2317.983166430062160298.770.1840.1480.1470.184random22.8
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]
0.09-0.30.1-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free12.127
r_sphericity_bonded9.17
r_scangle_it4.008
r_scbond_it3.418
r_angle_refined_deg2.749
r_rigid_bond_restr2.661
r_nbtor_refined0.296
r_symmetry_hbond_refined0.27
r_nbd_refined0.206
r_xyhbond_nbd_refined0.203
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free12.127
r_sphericity_bonded9.17
r_scangle_it4.008
r_scbond_it3.418
r_angle_refined_deg2.749
r_rigid_bond_restr2.661
r_nbtor_refined0.296
r_symmetry_hbond_refined0.27
r_nbd_refined0.206
r_xyhbond_nbd_refined0.203
r_chiral_restr0.149
r_symmetry_vdw_refined0.127
r_gen_planes_refined0.021
r_bond_refined_d0.018
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms830
Solvent Atoms194
Heterogen Atoms16

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling