X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 294.0
Details RNA WATER SOLUTION PLUS BUFFER (10 MM HEPES, 50 MM NACL, 0.5 MM TCEP, PH 7.0) MIXED 1:1 V/V WITH 2 M (NH4)2SO4 + 0.2 M NH4NO3 AND EQUILIBRATED AGAINST 2 M (NH4)2SO4 + 0.2 M NH4NO3, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 22.8 α = 90
b = 22.8 β = 90
c = 163.7 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
3 100
4 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 FOCUSING MIRRORS 2010-10-21
CCD ADSC QUANTUM 210 FOCUSING MIRRORS 2010-10-21
CCD ADSC QUANTUM 210 FOCUSING MIRRORS 2010-10-21
CCD MARMOSAIC 300 mm CCD FOCUSING MIRRORS 2010-05-29
Diffraction Radiation
Monochromator Protocol
Horizontal focusing 5.05 asymmetric cut Si(111) SINGLE WAVELENGTH
Horizontal focusing 5.05 asymmetric cut Si(111) SINGLE WAVELENGTH
Horizontal focusing 5.05 asymmetric cut Si(111) SINGLE WAVELENGTH
SI 111 DOUBLE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE A1 -- CHESS A1
SYNCHROTRON CHESS BEAMLINE A1 -- CHESS A1
SYNCHROTRON CHESS BEAMLINE A1 -- CHESS A1
SYNCHROTRON CLSI BEAMLINE 08ID-1 -- CLSI 08ID-1

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 41 92.6 0.0944 -- -- 2.73 23042 22972 4.0 -3.0 --
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)
1.0 1.1 73.1 0.1419 -- 4.72 1.2 --

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
AB INITIO PHASING 1.0 41.0 -- 1.0 23042 22972 1152 92.6 -- 0.126 0.118 0.158 RANDOM
RMS Deviations
Key Refinement Restraint Deviation
s_approx_iso_adps 0.1
s_similar_adp_cmpnt 0.015
s_rigid_bond_adp_cmpnt 0.005
s_anti_bump_dis_restr 0.021
s_from_restr_planes 0.038
s_angle_d 0.021
s_bond_d 0.007
Coordinate Error
Parameter Value
Number Disordered Residues 0.0
Occupancy Sum Hydrogen 242.0
Occupancy Sum Non Hydrogen 571.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 478
Heterogen Atoms 18
Solvent Atoms 76

Software

Computing
Computing Package Purpose
MxDC Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SHELXD Structure Solution
SHELXL Structure Refinement
Software
Software Name Purpose
SHELXL refinement
SHELXD model building
MxDC data collection