2D2L

Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X9C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293PEG 2000 MME, LITHIUM SULFATE, SPERMIDINE, COBALT HEXAAMINE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.170

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.2α = 90
b = 93.2β = 90
c = 122.19γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVConfocal Osmic2005-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R1.5418

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
12.530.7990.05129.612.91141211302-355.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5999.30.420.42713.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1X9C2.530.67-311412113029060.2260.2260.249RANDOM60.2
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]
-7.05-2.78-9.6816.73
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d17.6
c_improper_angle_d1.87
c_angle_deg1.4
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms1283
Solvent Atoms8
Heterogen Atoms26

Software

Software
Software NamePurpose
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing