X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Details 2.7 M 1,6-HEXANEDIOL, 200 MM AMMONIUM CHLORIDE, 10 MM MGCL2, 50 MM HEPES PH 8.0, 5 MM DTT.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 183.06 α = 90
b = 183.06 β = 90
c = 198.12 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL (PILATUS 6M-F) DECTRIS KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING 2011-07-03
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 -- DIAMOND I03

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
2.98 123.78 100.0 0.11 -- -- 10.1 -- 78522 -- -- 66.77
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)
2.98 3.06 100.0 0.83 -- 3.2 10.6 --

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 2.982 83.091 -- 1.22 -- 78400 7620 99.81 -- 0.2103 0.2078 0.2572 --
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 2.9816 3.0155 -- 248 4838 0.3251 0.3687 -- 100.0
X Ray Diffraction 3.0155 3.051 -- 267 4798 0.3139 0.3827 -- 100.0
X Ray Diffraction 3.051 3.0882 -- 257 4780 0.2874 0.3201 -- 100.0
X Ray Diffraction 3.0882 3.1273 -- 260 4773 0.281 0.3255 -- 100.0
X Ray Diffraction 3.1273 3.1685 -- 273 4811 0.2867 0.3428 -- 100.0
X Ray Diffraction 3.1685 3.2119 -- 310 4744 0.273 0.3285 -- 100.0
X Ray Diffraction 3.2119 3.2578 -- 232 4766 0.2765 0.3119 -- 100.0
X Ray Diffraction 3.2578 3.3064 -- 204 4857 0.2566 0.3309 -- 100.0
X Ray Diffraction 3.3064 3.358 -- 264 4709 0.2667 0.3266 -- 100.0
X Ray Diffraction 3.358 3.4131 -- 243 4859 0.2693 0.344 -- 100.0
X Ray Diffraction 3.4131 3.472 -- 222 4772 0.2579 0.3247 -- 100.0
X Ray Diffraction 3.472 3.5351 -- 258 4828 0.2454 0.3093 -- 100.0
X Ray Diffraction 3.5351 3.6031 -- 235 4791 0.2309 0.266 -- 100.0
X Ray Diffraction 3.6031 3.6766 -- 203 4785 0.2227 0.2942 -- 100.0
X Ray Diffraction 3.6766 3.7566 -- 241 4820 0.2162 0.2827 -- 100.0
X Ray Diffraction 3.7566 3.844 -- 300 4721 0.1979 0.239 -- 100.0
X Ray Diffraction 3.844 3.9401 -- 262 4809 0.1902 0.2553 -- 100.0
X Ray Diffraction 3.9401 4.0466 -- 275 4782 0.2062 0.2617 -- 100.0
X Ray Diffraction 4.0466 4.1657 -- 299 4750 0.1907 0.2316 -- 100.0
X Ray Diffraction 4.1657 4.3001 -- 240 4788 0.1734 0.2136 -- 100.0
X Ray Diffraction 4.3001 4.4538 -- 269 4804 0.1663 0.209 -- 100.0
X Ray Diffraction 4.4538 4.6321 -- 259 4767 0.1777 0.2303 -- 100.0
X Ray Diffraction 4.6321 4.8429 -- 225 4833 0.1695 0.2093 -- 100.0
X Ray Diffraction 4.8429 5.0982 -- 251 4780 0.1647 0.2013 -- 100.0
X Ray Diffraction 5.0982 5.4176 -- 247 4773 0.18 0.2499 -- 100.0
X Ray Diffraction 5.4176 5.8358 -- 220 4840 0.1953 0.2507 -- 100.0
X Ray Diffraction 5.8358 6.4229 -- 276 4773 0.1964 0.2766 -- 100.0
X Ray Diffraction 6.4229 7.3518 -- 251 4780 0.181 0.2262 -- 100.0
X Ray Diffraction 7.3518 9.2605 -- 283 4745 0.1595 0.1828 -- 100.0
X Ray Diffraction 9.2605 83.1234 -- 246 4736 0.219 0.247 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 56.38
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.084
f_dihedral_angle_d 18.898
f_angle_d 1.242
f_bond_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 18036
Nucleic Acid Atoms 903
Heterogen Atoms 16
Solvent Atoms 86

Software

Computing
Computing Package Purpose
XIA2, XDS Data Reduction (intensity integration)
XIA2, SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
PHASER model building