X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 295.0
Details 6% PEG8000, 18% isopropanol, 0.05 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.78 α = 90
b = 85.78 β = 90
c = 238.58 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-08-08
Diffraction Radiation
Monochromator Protocol
cryo-cooled double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C

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
3.1 100 97.7 0.097 -- -- -- 31133 30417 3.42 11.7 --
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)
3.1 3.21 95.5 0.537 -- 1.9 -- --

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 3.102 48.971 -- 1.38 25687 25687 1313 82.62 -- 0.1864 0.1803 0.2178 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 3.1052 3.2292 -- 73 1276 0.335 0.3511 -- 37.0
X Ray Diffraction 3.2292 3.3756 -- 94 1624 0.2489 0.3215 -- 47.0
X Ray Diffraction 3.3756 3.5528 -- 127 2375 0.2278 0.2662 -- 69.0
X Ray Diffraction 3.5528 3.7742 -- 174 3045 0.2061 0.2441 -- 89.0
X Ray Diffraction 3.7742 4.0638 -- 177 3155 0.1818 0.2082 -- 92.0
X Ray Diffraction 4.0638 4.4694 -- 147 3251 0.1618 0.19 -- 95.0
X Ray Diffraction 4.4694 5.1084 -- 158 3180 0.1673 0.25 -- 93.0
X Ray Diffraction 5.1084 6.4071 -- 178 3203 0.1849 0.2225 -- 93.0
X Ray Diffraction 6.4071 21.3601 -- 185 3168 0.1607 0.1853 -- 91.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.056
f_dihedral_angle_d 16.727
f_angle_d 0.828
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11380
Nucleic Acid Atoms 1464
Heterogen Atoms 134
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.2_1309) refinement
PHASES model building
HKL-2000 data collection