1NTA

2.9 A crystal structure of Streptomycin RNA-aptamer


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6298MES buffer, barium cloride, magnesium cloride, sodium cloride, MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3563.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.097α = 90
b = 83.097β = 90
c = 49.472γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2002-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
12.93099.70.0549.54018
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.852.95990.65

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.920342335699.160.227880.222340.28169RANDOM44.59
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]
0.390.39-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it2.181
r_angle_refined_deg1.782
r_scbond_it1.406
r_angle_other_deg0.913
r_symmetry_vdw_other0.297
r_nbd_other0.246
r_xyhbond_nbd_refined0.208
r_nbd_refined0.19
r_symmetry_vdw_refined0.154
r_symmetry_hbond_refined0.124
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it2.181
r_angle_refined_deg1.782
r_scbond_it1.406
r_angle_other_deg0.913
r_symmetry_vdw_other0.297
r_nbd_other0.246
r_xyhbond_nbd_refined0.208
r_nbd_refined0.19
r_symmetry_vdw_refined0.154
r_symmetry_hbond_refined0.124
r_chiral_restr0.119
r_nbtor_other0.092
r_bond_refined_d0.012
r_gen_planes_refined0.009
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 Atoms842
Solvent Atoms
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing