1N7A

RIP-Radiation-damage Induced Phasing


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62981 mM (single strand) RNA, 20 mM sodium cacodylate buffer, pH 6.0, 5 mM spermine tetrachloride, 32 mM KCl and 2 % (v/v) methyl-2,4-pentanediol (MPD) against 25 % MPD in the reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.7730.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.233α = 90
b = 51.102β = 90
c = 70.651γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.22099.50.08710.834.243597435974-34.9
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)
1.21.2798.50.3413.824.195469

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.2203597435974180299.710.125330.125330.123690.15626RANDOM9.356
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]
0.020.2-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded4.684
r_sphericity_free2.853
r_scangle_it2.79
r_scbond_it2.12
r_angle_refined_deg1.533
r_rigid_bond_restr1.164
r_nbd_refined0.374
r_symmetry_hbond_refined0.144
r_symmetry_vdw_refined0.133
r_xyhbond_nbd_refined0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded4.684
r_sphericity_free2.853
r_scangle_it2.79
r_scbond_it2.12
r_angle_refined_deg1.533
r_rigid_bond_restr1.164
r_nbd_refined0.374
r_symmetry_hbond_refined0.144
r_symmetry_vdw_refined0.133
r_xyhbond_nbd_refined0.081
r_chiral_restr0.072
r_gen_planes_refined0.019
r_bond_refined_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms1024
Solvent Atoms181
Heterogen Atoms31

Software

Software
Software NamePurpose
ProDCdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
REFMACrefinement
XDSdata scaling