X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 0.12M 1,6-Hexanediol; 0.12M 1-Butanol; 0.12M 1,2-Propanediol (racemic); 0.12M 2-Propanol; 0.12M 1,4-Butanediol; 0.12M 1,3-Propanediol, 55.5 mM MES pH 3.11, 44.5 mM imidazole pH 10.23; 12.5% w/v PEG 1000; 12.5% w/v PEG 3350; 12.5% v/v MPD

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.88 α = 90
b = 59.88 β = 90
c = 159.93 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2018-04-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1

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
2.9 49.33 100.0 -- -- -- 56.6 -- 7915 -- -- --
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)
2.9 3.08 100.0 -- -- 2.3 55.1 --

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
SAD 2.9 49.329 -- 1.94 -- 14237 1419 99.89 -- 0.2589 0.2542 0.3039 --
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 2.9002 3.0038 -- 138 1319 0.3467 0.3423 -- 100.0
X Ray Diffraction 3.0038 3.1241 -- 146 1288 0.3472 0.3935 -- 100.0
X Ray Diffraction 3.1241 3.2662 -- 148 1240 0.3174 0.3523 -- 100.0
X Ray Diffraction 3.2662 3.4384 -- 146 1289 0.3047 0.3426 -- 100.0
X Ray Diffraction 3.4384 3.6538 -- 134 1268 0.2827 0.3329 -- 100.0
X Ray Diffraction 3.6538 3.9358 -- 140 1296 0.269 0.3343 -- 100.0
X Ray Diffraction 3.9358 4.3316 -- 145 1292 0.2384 0.301 -- 100.0
X Ray Diffraction 4.3316 4.9579 -- 142 1271 0.1973 0.2674 -- 100.0
X Ray Diffraction 4.9579 6.2445 -- 136 1272 0.2479 0.2453 -- 100.0
X Ray Diffraction 6.2445 49.3363 -- 144 1283 0.2515 0.323 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_plane_restr 0.004
f_angle_d 0.539
f_dihedral_angle_d 18.511
f_chiral_restr 0.046
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2197
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement version: (dev_3126: ???)
XDS data reduction
XSCALE data scaling
PHENIX phasing