X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Evaporation
pH 6.2
Temperature 298.0
Details 0.1 M phosphate (pH 6.2), and 15% (w/v) PEG3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.08 α = 90
b = 196.99 β = 90
c = 116.24 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2018-04-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 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
1.9 47.04 99.4 0.06 -- -- 3.715 -- 143553 -- -- 31.86
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)
1.9 2.02 98.9 0.636 -- 1.86 3.798 --

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
-- 1.903 47.038 -- 1.35 -- 143441 2153 99.24 -- 0.1947 0.1941 0.2347 --
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 1.9027 1.947 -- 141 9022 0.3138 0.344 0.0 96.0
X Ray Diffraction 1.947 1.9957 -- 141 9373 0.2971 0.3524 0.0 100.0
X Ray Diffraction 1.9957 2.0497 -- 141 9374 0.2651 0.2904 0.0 100.0
X Ray Diffraction 2.0497 2.11 -- 143 9327 0.248 0.2589 0.0 99.0
X Ray Diffraction 2.11 2.1781 -- 144 9329 0.2357 0.2968 0.0 99.0
X Ray Diffraction 2.1781 2.2559 -- 142 9371 0.224 0.2568 0.0 100.0
X Ray Diffraction 2.2559 2.3462 -- 145 9431 0.2101 0.2439 0.0 100.0
X Ray Diffraction 2.3462 2.453 -- 142 9427 0.2095 0.2705 0.0 100.0
X Ray Diffraction 2.453 2.5823 -- 145 9457 0.2044 0.2165 0.0 100.0
X Ray Diffraction 2.5823 2.7441 -- 143 9352 0.201 0.2666 0.0 99.0
X Ray Diffraction 2.7441 2.956 -- 143 9480 0.2034 0.2472 0.0 99.0
X Ray Diffraction 2.956 3.2534 -- 145 9473 0.195 0.2542 0.0 100.0
X Ray Diffraction 3.2534 3.724 -- 148 9521 0.1788 0.2076 0.0 99.0
X Ray Diffraction 3.724 4.6911 -- 143 9511 0.1491 0.183 0.0 99.0
X Ray Diffraction 4.6911 47.0525 -- 147 9840 0.1744 0.214 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.3009
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.98
f_bond_d 0.011
f_chiral_restr 0.203
f_plane_restr 0.006
f_dihedral_angle_d 20.184
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11699
Nucleic Acid Atoms 0
Heterogen Atoms 187
Solvent Atoms 938

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: 1.12_2829
PDB_EXTRACT data extraction version: 3.24
XDS data reduction
PHENIX phasing