X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 277.0
Details SPG buffer 0.1M pH4.0, 15% Peg 1500, drop volumes 200nl plus 200nl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.91 α = 90
b = 95.01 β = 90
c = 230.29 γ = 90
Symmetry
Space Group P 2 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-03-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I02 0.9173 DIAMOND I02

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
2.2 29.86 -- -- -- -- -- -- 62077 -- -- --
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)
2.2 2.33 97.3 -- -- -- -- --

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 2.2 29.86 -- 2.0 -- 62063 2000 99.43 -- 0.1762 0.1748 0.2168 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 2.2 2.2522 -- 131 3957 0.2234 0.2932 -- 95.0
X Ray Diffraction 2.2522 2.313 -- 141 4241 0.2036 0.2827 -- 100.0
X Ray Diffraction 2.313 2.3811 -- 145 4306 0.1929 0.2684 -- 100.0
X Ray Diffraction 2.3811 2.4579 -- 139 4216 0.1888 0.268 -- 100.0
X Ray Diffraction 2.4579 2.5457 -- 143 4278 0.1975 0.224 -- 100.0
X Ray Diffraction 2.5457 2.6476 -- 142 4270 0.1775 0.2339 -- 100.0
X Ray Diffraction 2.6476 2.768 -- 143 4278 0.181 0.2209 -- 100.0
X Ray Diffraction 2.768 2.9138 -- 141 4271 0.1802 0.2334 -- 100.0
X Ray Diffraction 2.9138 3.0962 -- 144 4290 0.1892 0.2388 -- 100.0
X Ray Diffraction 3.0962 3.3349 -- 143 4291 0.1851 0.2482 -- 99.0
X Ray Diffraction 3.3349 3.67 -- 144 4354 0.1752 0.2063 -- 100.0
X Ray Diffraction 3.67 4.1998 -- 145 4341 0.1471 0.1751 -- 100.0
X Ray Diffraction 4.1998 5.2865 -- 145 4384 0.1405 0.1948 -- 100.0
X Ray Diffraction 5.2865 29.8667 -- 154 4586 0.1802 0.1684 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.078
f_dihedral_angle_d 13.067
f_angle_d 1.131
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8079
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 577

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
Phaser model building
DNA data collection