X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 6.5
Temperature 298.0
Details 17% MPD

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 400.97 α = 90
b = 400.97 β = 90
c = 175.05 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2017-04-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.98 SSRL BL12-2

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
3.12 39.91 97.7 1.011 -- -- 97.904 -- 244903 -- -- 127.69
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)
3.12 3.2 70.9 17.255 -- 0.19 43.218 --

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
-- 3.4 39.908 -- 1.33 -- 193729 1580 99.81 -- 0.1833 0.1829 0.2298 --
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 3.4 3.5097 -- 143 17313 0.3527 0.401 0.0 100.0
X Ray Diffraction 3.5097 3.635 -- 141 17300 0.3258 0.3313 0.0 100.0
X Ray Diffraction 3.635 3.7805 -- 143 17344 0.2917 0.3467 0.0 100.0
X Ray Diffraction 3.7805 3.9524 -- 142 17303 0.264 0.286 0.0 100.0
X Ray Diffraction 3.9524 4.1606 -- 144 17401 0.224 0.294 0.0 100.0
X Ray Diffraction 4.1606 4.4209 -- 143 17387 0.1901 0.2518 0.0 100.0
X Ray Diffraction 4.4209 4.7618 -- 143 17449 0.1731 0.2122 0.0 100.0
X Ray Diffraction 4.7618 5.24 -- 144 17471 0.1523 0.1948 0.0 100.0
X Ray Diffraction 5.24 5.996 -- 145 17581 0.1413 0.1898 0.0 100.0
X Ray Diffraction 5.996 7.546 -- 146 17675 0.15 0.2264 0.0 100.0
X Ray Diffraction 7.546 39.9107 -- 146 17925 0.148 0.1808 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 142.397
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.937
f_chiral_restr 0.043
f_angle_d 0.823
f_bond_d 0.004
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32943
Heterogen Atoms 507
Solvent Atoms 0

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHENIX refinement
PDB_EXTRACT data extraction version: 3.24
PHENIX phasing