X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 298.0
Details trisodium citrate dihydrate, 2-propanol, PEG 10,000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.96 α = 90
b = 90.96 β = 90
c = 316.32 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2014-12-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1

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
1.46 70.51 99.8 0.138 -- -- 21.5 -- 134366 -- -- 13.36
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)
1.46 1.5 99.2 1.704 -- 2.3 21.7 --

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 1.46 70.51 -- 1.34 -- 134282 2000 99.7 -- 0.14 0.14 0.151 --
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 1.46 1.4965 -- 139 9231 0.2281 0.2498 -- 99.0
X Ray Diffraction 1.4965 1.537 -- 140 9222 0.2047 0.2081 -- 99.0
X Ray Diffraction 1.537 1.5822 -- 140 9261 0.1875 0.1687 -- 99.0
X Ray Diffraction 1.5822 1.6333 -- 140 9263 0.1721 0.207 -- 99.0
X Ray Diffraction 1.6333 1.6917 -- 141 9338 0.158 0.1879 -- 99.0
X Ray Diffraction 1.6917 1.7594 -- 141 9321 0.1481 0.1945 -- 100.0
X Ray Diffraction 1.7594 1.8395 -- 142 9351 0.1391 0.1498 -- 100.0
X Ray Diffraction 1.8395 1.9365 -- 142 9409 0.1319 0.1367 -- 100.0
X Ray Diffraction 1.9365 2.0578 -- 143 9413 0.1293 0.1515 -- 100.0
X Ray Diffraction 2.0578 2.2167 -- 142 9477 0.1227 0.1312 -- 100.0
X Ray Diffraction 2.2167 2.4398 -- 144 9494 0.1179 0.1355 -- 100.0
X Ray Diffraction 2.4398 2.7928 -- 144 9573 0.1238 0.1626 -- 100.0
X Ray Diffraction 2.7928 3.5187 -- 148 9716 0.1272 0.1295 -- 100.0
X Ray Diffraction 3.5187 70.5942 -- 154 10213 0.1448 0.138 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.68
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_angle_d 0.924
f_dihedral_angle_d 16.364
f_bond_d 0.007
f_chiral_restr 0.076
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4255
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 799

Software

Software
Software Name Purpose
PHENIX refinement version: DEV_2447
xia2 data scaling version: 0.3.8.0
PDB_EXTRACT data extraction version: 3.22
xia2 data reduction
PHENIX phasing