X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 291.0
Details PEG4000, Isopropanol, Sodium Citrate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.55 α = 90
b = 65.54 β = 92.72
c = 55.12 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 2M -- 2017-11-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.459 LNLS W01B-MX2

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
1.69 55.06 94.5 0.049 -- -- 3.3 -- 29583 -- -- 18.47
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)
1.69 1.78 89.8 0.382 -- -- 3.1 --

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 1.693 18.884 -- 1.34 -- 29545 1441 94.15 -- 0.1805 0.1786 0.2183 --
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 1.6931 1.7536 -- 129 2634 0.2369 0.2892 0.0 89.0
X Ray Diffraction 1.7536 1.8238 -- 135 2759 0.23 0.2743 0.0 92.0
X Ray Diffraction 1.8238 1.9067 -- 150 2749 0.1861 0.2256 0.0 93.0
X Ray Diffraction 1.9067 2.0071 -- 141 2762 0.2026 0.2527 0.0 93.0
X Ray Diffraction 2.0071 2.1327 -- 155 2806 0.1762 0.2577 0.0 95.0
X Ray Diffraction 2.1327 2.2971 -- 139 2827 0.1932 0.2278 0.0 94.0
X Ray Diffraction 2.2971 2.5278 -- 144 2873 0.1798 0.2454 0.0 96.0
X Ray Diffraction 2.5278 2.8924 -- 156 2877 0.1777 0.2178 0.0 96.0
X Ray Diffraction 2.8924 3.6399 -- 145 2889 0.1678 0.1919 0.0 96.0
X Ray Diffraction 3.6399 18.8853 -- 147 2928 0.16 0.1848 0.0 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.2438
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.946
f_bond_d 0.013
f_chiral_restr 0.065
f_plane_restr 0.008
f_angle_d 1.216
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1908
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 314

Software

Software
Software Name Purpose
Aimless data scaling version: 0.5.32
PHASER phasing version: 2.8.0
PHENIX refinement version: 1.12
PDB_EXTRACT data extraction version: 3.24
AutoPROC data collection version: 1.0.5