1R3O | pdb_00001r3o

Crystal structure of the first RNA duplex in L-conformation at 1.9A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17pH 7.0, temperature 100K
Crystal Properties
Matthews coefficientSolvent content
2.6353.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.109α = 90
b = 46.109β = 90
c = 263.501γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.920.540.0658385

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.920.5479963881000.240820.238550.240.285630.31RANDOM32.841
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]
0.780.390.78-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_chiral_restr5.108
r_scangle_it2.33
r_angle_refined_deg1.766
r_scbond_it1.746
r_angle_other_deg1.343
r_symmetry_hbond_refined0.22
r_nbd_other0.211
r_xyhbond_nbd_refined0.173
r_symmetry_vdw_other0.12
r_nbd_refined0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_chiral_restr5.108
r_scangle_it2.33
r_angle_refined_deg1.766
r_scbond_it1.746
r_angle_other_deg1.343
r_symmetry_hbond_refined0.22
r_nbd_other0.211
r_xyhbond_nbd_refined0.173
r_symmetry_vdw_other0.12
r_nbd_refined0.098
r_nbtor_other0.055
r_symmetry_vdw_refined0.053
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_mcbond_it
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 Atoms676
Solvent Atoms129
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling