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 = 31.25 α = 90
b = 51.15 β = 90
c = 70.83 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
1.4 20 99.3 0.095 -- -- 4.25 22939 22939 0.0 -3.0 6.4
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)
1.4 1.48 98.1 0.465 -- 3.1 4.24 3438

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
RIP - Radiation-damage Induced Phasing 1.4 20.0 -3.0 0.0 22939 22939 1148 99.44 0.15453 0.15453 0.15216 0.19949 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 1.4 1.476 -- 155 3104 0.194 0.286 -- --
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 9.645
Anisotropic B[1][1] -0.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.25
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.021
r_bond_refined_d 0.018
r_chiral_restr 0.108
r_nbd_refined 0.412
r_scbond_it 3.131
r_scangle_it 3.844
r_sphericity_bonded 5.791
r_angle_refined_deg 1.935
r_xyhbond_nbd_refined 0.119
r_rigid_bond_restr 2.128
r_sphericity_free 4.347
r_symmetry_hbond_refined 0.185
r_symmetry_vdw_refined 0.138
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
XDS data scaling