X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 277.0
Details 50 mM Tris pH 8.5, 10% P8K, 1 mM TCEP, 6% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.31 α = 90
b = 107.88 β = 90
c = 179.95 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
AREA DETECTOR ADSC QUANTUM 315r -- 2009-03-17
Diffraction Radiation
Monochromator Protocol
Si III SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980100 SOLEIL PROXIMA 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
2.6 19.98 99.6 -- -- -- -- 44722 44526 -3.0 -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)
2.6 2.7 99.9 -- -- -- -- --

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
MOLECULAR REPLACEMENT 2.6 19.975 -- 1.99 44722 44524 2227 99.84 -- 0.1723 0.1696 0.2235 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 2.6 2.6927 -- 220 4170 0.2571 0.3256 -- 100.0
X Ray Diffraction 2.6927 2.8003 -- 219 4161 0.2314 0.2799 -- 100.0
X Ray Diffraction 2.8003 2.9273 -- 220 4181 0.2256 0.3121 -- 100.0
X Ray Diffraction 2.9273 3.0811 -- 221 4202 0.2116 0.2884 -- 100.0
X Ray Diffraction 3.0811 3.2734 -- 220 4187 0.1881 0.2379 -- 100.0
X Ray Diffraction 3.2734 3.5249 -- 221 4201 0.1789 0.2419 -- 100.0
X Ray Diffraction 3.5249 3.8773 -- 223 4222 0.1678 0.2208 -- 100.0
X Ray Diffraction 3.8773 4.433 -- 222 4225 0.1365 0.1727 -- 100.0
X Ray Diffraction 4.433 5.565 -- 227 4315 0.14 0.1891 -- 100.0
X Ray Diffraction 5.565 19.975 -- 234 4433 0.1512 0.2024 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.07
f_dihedral_angle_d 15.476
f_angle_d 1.095
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7099
Nucleic Acid Atoms 0
Heterogen Atoms 51
Solvent Atoms 392

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
molrep Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
molrep model building
DNA data collection