X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 295.15
Details 25% PEG4000, 0.17M Ammonium acetate, 0.085 sodium citrate pH 5.6

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.84 α = 90
b = 56.39 β = 90
c = 126.15 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
PIXEL DECTRIS EIGER X 16M iger 1M with max frame rate of 133 Hz: Count rate 2MHz/pixel. Mini-beam 5 or 10 micron beam 2016-03-11
Diffraction Radiation
Monochromator Protocol
Si(111) Khozu SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B

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
1.55 42.25 99.9 0.07 -- -- 9.6 -- 47198 -- -- 25.1
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)
1.55 1.58 99.4 0.953 -- -- 6.2 --

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 1.551 42.253 -- 1.36 -- 47114 2000 99.75 -- 0.1696 0.1689 0.1851 --
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 1.5509 1.5897 -- 136 3066 0.285 0.2965 0.0 97.0
X Ray Diffraction 1.5897 1.6326 -- 142 3196 0.2496 0.2841 0.0 100.0
X Ray Diffraction 1.6326 1.6807 -- 141 3190 0.226 0.2489 0.0 100.0
X Ray Diffraction 1.6807 1.7349 -- 141 3187 0.2028 0.2148 0.0 100.0
X Ray Diffraction 1.7349 1.7969 -- 142 3198 0.1858 0.1866 0.0 100.0
X Ray Diffraction 1.7969 1.8689 -- 142 3192 0.1789 0.206 0.0 100.0
X Ray Diffraction 1.8689 1.954 -- 141 3190 0.1697 0.2149 0.0 100.0
X Ray Diffraction 1.954 2.057 -- 143 3208 0.161 0.183 0.0 100.0
X Ray Diffraction 2.057 2.1858 -- 141 3203 0.1584 0.1841 0.0 100.0
X Ray Diffraction 2.1858 2.3546 -- 143 3240 0.1647 0.1596 0.0 100.0
X Ray Diffraction 2.3546 2.5915 -- 143 3220 0.1678 0.1667 0.0 100.0
X Ray Diffraction 2.5915 2.9664 -- 146 3279 0.1673 0.1764 0.0 100.0
X Ray Diffraction 2.9664 3.737 -- 146 3301 0.161 0.1748 0.0 100.0
X Ray Diffraction 3.737 42.2684 -- 153 3444 0.1619 0.1874 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.5981
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.06
f_bond_d 0.008
f_plane_restr 0.006
f_angle_d 0.968
f_dihedral_angle_d 19.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1925
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 111

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
HKL-2000 data reduction
SCALEPACK data scaling
PDB_EXTRACT data extraction version: 3.22
Coot model building
PHASER phasing