2OE5

1.5 A X-ray crystal structure of Apramycin complex with RNA fragment GGCGUCGCUAGUACCG/GGUACUAAAAGUCGCCC containing the human ribosomal decoding A site: RNA construct with 3'-overhang


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOtherSTANDARD RNA-MODEL BUILT IN TURBO-FRODO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62980.05M MES BUFFER, 15-20% MPD, 0.02-0.04M MAGNESIUM ACETATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1342.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.31α = 90
b = 36.693β = 90
c = 86.679γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42000-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9A1.0000NSLSX9A

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
11.52092.731386513865

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSTANDARD RNA-MODEL BUILT IN TURBO-FRODO1.5119.92131731317369292.730.200060.198760.2268RANDOM20.524
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]
0.02-0.060.04
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it2.535
r_scbond_it1.873
r_angle_refined_deg1.793
r_angle_other_deg1.746
r_chiral_restr0.871
r_symmetry_hbond_refined0.247
r_xyhbond_nbd_refined0.216
r_nbd_other0.206
r_symmetry_vdw_other0.203
r_nbd_refined0.124
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it2.535
r_scbond_it1.873
r_angle_refined_deg1.793
r_angle_other_deg1.746
r_chiral_restr0.871
r_symmetry_hbond_refined0.247
r_xyhbond_nbd_refined0.216
r_nbd_other0.206
r_symmetry_vdw_other0.203
r_nbd_refined0.124
r_symmetry_vdw_refined0.112
r_metal_ion_refined0.065
r_xyhbond_nbd_other0.05
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbtor_refined
r_nbtor_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms698
Solvent Atoms164
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing