X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 100 mM HEPES, 30 % PEG 1000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.6 α = 90
b = 58.09 β = 90
c = 103.27 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 PILATUS 6M -- 2017-10-25
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1 ESRF ID23-1

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
1.65 38.59 97.2 0.1 -- -- 2.753 -- 27933 -- -- 16.87
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)
1.65 1.69 99.0 0.507 -- 1.82 2.741 --

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 1.65 38.593 -- 1.36 -- 27927 1396 97.13 -- 0.1693 0.1675 0.2039 --
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 1.6498 1.7088 -- 139 2651 0.2485 0.2602 0.0 98.0
X Ray Diffraction 1.7088 1.7772 -- 137 2608 0.2273 0.2925 0.0 97.0
X Ray Diffraction 1.7772 1.8581 -- 141 2666 0.2052 0.2629 0.0 99.0
X Ray Diffraction 1.8581 1.9561 -- 140 2671 0.1869 0.2355 0.0 99.0
X Ray Diffraction 1.9561 2.0786 -- 141 2680 0.1784 0.236 0.0 99.0
X Ray Diffraction 2.0786 2.2391 -- 138 2622 0.1682 0.2269 0.0 97.0
X Ray Diffraction 2.2391 2.4644 -- 140 2660 0.1666 0.237 0.0 98.0
X Ray Diffraction 2.4644 2.8209 -- 139 2642 0.1647 0.2124 0.0 96.0
X Ray Diffraction 2.8209 3.5536 -- 140 2669 0.1512 0.173 0.0 96.0
X Ray Diffraction 3.5536 38.6032 -- 141 2662 0.1449 0.1549 0.0 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.4289
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_dihedral_angle_d 9.981
f_angle_d 0.786
f_bond_d 0.004
f_chiral_restr 0.053
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1774
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 269

Software

Software
Software Name Purpose
XDS data reduction version: VERSION Jun 1, 2017
XSCALE data scaling version: VERSION Jun 1, 2017
PHENIX refinement version: 1.11
PDB_EXTRACT data extraction version: 3.24
PHASER phasing version: 2.7.16