X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 1 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 Data

Unit Cell
Length (Å) Angle (°)
a = 31.23 α = 90
b = 51.1 β = 90
c = 70.65 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-02-08
Diffraction Radiation
Monochromator Protocol
diamond(111) and Ge(200) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.2 20 99.5 0.087 -- -- 4.24 35974 35974 0.0 -3.0 4.9
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.2 1.27 98.5 0.341 -- 3.82 4.19 5469

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
-- 1.2 20.0 0.0 0.0 35974 35974 1802 99.71 0.12533 0.12533 0.12369 0.15626 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.201 1.265 -- 268 4872 0.167 0.208 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model The DNA/RNA and K-atoms were refined anisotropically, the spermine and waters isotropic
Mean Isotropic B 9.356
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.22
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.081
r_scbond_it 2.12
r_rigid_bond_restr 1.164
r_sphericity_bonded 4.684
r_nbd_refined 0.374
r_gen_planes_refined 0.019
r_bond_refined_d 0.01
r_angle_refined_deg 1.533
r_symmetry_vdw_refined 0.133
r_scangle_it 2.79
r_sphericity_free 2.853
r_chiral_restr 0.072
r_symmetry_hbond_refined 0.144
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 1024
Heterogen Atoms 31
Solvent Atoms 181

Software

Software
Software Name Purpose
prodc data collection
XDS data reduction
SHELXD phasing
SHARP phasing
REFMAC refinement version: 5.1.24
PRODC data reduction
XDS data scaling