X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 0.1 M Imidazol, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.27 α = 90
b = 79.13 β = 100.27
c = 69.07 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-08-08
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
1.48 29.08 99.7 -- 0.057 -- 3.7 114707 114707 -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)
1.48 1.52 99.8 -- 0.647 2.4 3.7 --

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 1.48 29.08 -- 0.0 114698 114698 5772 99.78 -- 0.1857 0.1848 0.2038 --
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 1.48 1.4968 -- 203 3590 0.2892 0.296 -- 100.0
X Ray Diffraction 1.4968 1.5144 -- 202 3605 0.2796 0.2895 -- 100.0
X Ray Diffraction 1.5144 1.5329 -- 194 3608 0.2684 0.326 -- 100.0
X Ray Diffraction 1.5329 1.5523 -- 186 3652 0.2532 0.2527 -- 100.0
X Ray Diffraction 1.5523 1.5727 -- 191 3579 0.2452 0.2503 -- 100.0
X Ray Diffraction 1.5727 1.5943 -- 174 3652 0.2323 0.2761 -- 100.0
X Ray Diffraction 1.5943 1.617 -- 212 3573 0.2347 0.2733 -- 100.0
X Ray Diffraction 1.617 1.6412 -- 191 3664 0.2231 0.2486 -- 100.0
X Ray Diffraction 1.6412 1.6668 -- 211 3585 0.2161 0.2369 -- 100.0
X Ray Diffraction 1.6668 1.6941 -- 192 3645 0.2034 0.2471 -- 100.0
X Ray Diffraction 1.6941 1.7234 -- 188 3631 0.2012 0.2015 -- 100.0
X Ray Diffraction 1.7234 1.7547 -- 167 3625 0.1897 0.2188 -- 100.0
X Ray Diffraction 1.7547 1.7884 -- 200 3613 0.1814 0.2081 -- 100.0
X Ray Diffraction 1.7884 1.8249 -- 194 3616 0.1824 0.2073 -- 100.0
X Ray Diffraction 1.8249 1.8646 -- 198 3662 0.1781 0.2015 -- 100.0
X Ray Diffraction 1.8646 1.908 -- 190 3598 0.1779 0.2301 -- 100.0
X Ray Diffraction 1.908 1.9557 -- 210 3603 0.1765 0.1865 -- 100.0
X Ray Diffraction 1.9557 2.0085 -- 197 3648 0.1759 0.1936 -- 100.0
X Ray Diffraction 2.0085 2.0676 -- 177 3634 0.1787 0.1997 -- 100.0
X Ray Diffraction 2.0676 2.1343 -- 178 3665 0.1791 0.2311 -- 100.0
X Ray Diffraction 2.1343 2.2106 -- 194 3612 0.176 0.1834 -- 100.0
X Ray Diffraction 2.2106 2.2991 -- 208 3620 0.1747 0.1878 -- 100.0
X Ray Diffraction 2.2991 2.4037 -- 214 3617 0.1736 0.198 -- 100.0
X Ray Diffraction 2.4037 2.5303 -- 191 3621 0.1773 0.1946 -- 100.0
X Ray Diffraction 2.5303 2.6888 -- 180 3652 0.1839 0.2024 -- 100.0
X Ray Diffraction 2.6888 2.8962 -- 195 3642 0.1829 0.2056 -- 100.0
X Ray Diffraction 2.8962 3.1873 -- 172 3668 0.1755 0.1924 -- 100.0
X Ray Diffraction 3.1873 3.6478 -- 189 3675 0.1723 0.1938 -- 100.0
X Ray Diffraction 3.6478 4.5929 -- 206 3628 0.154 0.1641 -- 99.0
X Ray Diffraction 4.5929 29.0855 -- 168 3743 0.1836 0.186 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic, TLS
Anisotropic B[1][1] -0.351
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.9715
Anisotropic B[2][2] -1.1312
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.4822
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.075
f_dihedral_angle_d 14.799
f_angle_d 1.12
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4823
Nucleic Acid Atoms 0
Heterogen Atoms 139
Solvent Atoms 765

Software

Computing
Computing Package Purpose
SERGUI Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER (2.1.4) Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
PHASER version: (2.1.4) model building
SERGUI data collection