2P7F

The Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small Ribozyme


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZFRPDB ENTRY 1ZFR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293250 mM Li2SO4, 2.5 mM [Co(NH3)6]Cl3, 2 mM spermidine-HCl, 15 mM nicotinic acid, 100 mM sodium HEPES buffer and 20.5% PEG 2000 MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.1179.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.1α = 90
b = 94.1β = 90
c = 127.2γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)2006-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97945SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.3540.7699.10.03719.65.921432114321-390.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.352.4399.10.4482.95.32

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1ZFR2.3529.381431314313724990.2260.2260.2270.252RANDOM81.7
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]
-13.01-2.59-13.0126.02
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d17.3
c_improper_angle_d1.86
c_angle_deg1.4
c_bond_d0.008
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms1310
Solvent Atoms15
Heterogen Atoms19

Software

Software
Software NamePurpose
Blu-Icedata collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing