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_sphericity_bonded 5.791
r_bond_refined_d 0.018
r_angle_refined_deg 1.935
r_chiral_restr 0.108
r_gen_planes_refined 0.021
r_nbd_refined 0.412
r_xyhbond_nbd_refined 0.119
r_symmetry_vdw_refined 0.138
r_symmetry_hbond_refined 0.185
r_scbond_it 3.131
r_scangle_it 3.844
r_rigid_bond_restr 2.128
r_sphericity_free 4.347
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

Computing
Computing Package Purpose
PRODC Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
SHELXD, SHARP Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
sharp model building
shelxd model building
XDS data reduction
prodc data collection