2GRB

Crystal Structure of an RNA Quadruplex Containing Inosine-tetrad


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7298KCl, CaCl2, MPD , pH 7.0, EVAPORATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8232.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.06α = 90
b = 52.738β = 102.98
c = 37.344γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 2102003-07-09MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-D0.9195,0.9200,0.8984APS14-BM-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.43095.36.8723152
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4571.5

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 DIFFRACTIONMADTHROUGHOUT1.481950919509100695.230.197810.197810.195140.25002RANDOM29.058
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]
0.36-1.66-2.351.24
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free3.507
r_sphericity_bonded3.436
r_scangle_it3.07
r_angle_refined_deg2.78
r_scbond_it2.488
r_rigid_bond_restr1.969
r_nbd_refined0.351
r_chiral_restr0.291
r_symmetry_metal_ion_refined0.283
r_nbtor_refined0.265
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free3.507
r_sphericity_bonded3.436
r_scangle_it3.07
r_angle_refined_deg2.78
r_scbond_it2.488
r_rigid_bond_restr1.969
r_nbd_refined0.351
r_chiral_restr0.291
r_symmetry_metal_ion_refined0.283
r_nbtor_refined0.265
r_xyhbond_nbd_refined0.254
r_metal_ion_refined0.176
r_symmetry_vdw_refined0.163
r_symmetry_hbond_refined0.127
r_gen_planes_refined0.012
r_bond_refined_d0.01
r_symmetry_metal_ion_other
r_bond_other_d
r_metal_ion_other
r_nbd_other
r_symmetry_vdw_other
r_gen_planes_other
r_symmetry_hbond_other
r_dihedral_angle_4_deg
r_nbtor_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_dihedral_angle_3_deg
r_dihedral_angle_2_deg
r_dihedral_angle_1_deg
r_angle_other_deg
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms970
Solvent Atoms178
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
d*TREKdata scaling
SOLVEphasing