X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details 1 microliter of 10 mM cylinder, 1 microliter of 3 mM DNA, 2 microliters of crystallization buffer (10 mM Magnesium chloride, 5% v/v Isopropanol, 50 mM Tris-HCl), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.25 α = 90
b = 49.25 β = 90
c = 49.25 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2006-02-23
Diffraction Radiation
Monochromator Protocol
Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 1.7366, 1.7410, 1.7311 ESRF ID29

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
2.44 24.63 99.4 0.041 -- -- 8.4 1573 1573 0.0 -3.0 94.0
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)
2.44 2.58 100.0 0.447 -- 2.2 5.1 228

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
MAD 2.44 24.63 -- -- 1573 1540 74 98.0 0.187 0.187 0.187 0.212 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 2.44 2.55 165 -- -- 0.358 -- -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 79.4
RMS Deviations
Key Refinement Restraint Deviation
s_from_restr_planes 0.031
s_bond_d 0.006
s_non_zero_chiral_vol 0.006
s_anti_bump_dis_restr 0.005
s_angle_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 120
Heterogen Atoms 62
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ProDC Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHELXD/E Structure Solution
SHELXL-97 Structure Refinement
Software
Software Name Purpose
SHELXL-97 refinement
SHELXD/E model building
ProDC data collection