X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Temperature 298.0
Details Protein crystallized from 1.9M Sodium/Potassium Phosphate, Batch method, pH 7.0, LIQUID DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.43 α = 90
b = 53.43 β = 90
c = 192.22 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D -- APS 21-ID-D

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
1.68 51.48 74.0 0.127 -- -- 10.13 -- 24312 -- -- 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)
1.68 1.74 17.2 0.42 -- 2.3 3.52 --

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
FOURIER SYNTHESIS 1.68 51.48 -- 1.34 -- 24302 2000 74.0 -- 0.203 0.199 0.243 --
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 1.6808 1.7228 -- 28 313 0.4448 0.4934 -- 15.0
X Ray Diffraction 1.7228 1.7694 -- 47 520 0.3339 0.4505 -- 25.0
X Ray Diffraction 1.7694 1.8214 -- 64 711 0.319 0.3619 -- 34.0
X Ray Diffraction 1.8214 1.8802 -- 83 938 0.2755 0.3034 -- 44.0
X Ray Diffraction 1.8802 1.9474 -- 110 1225 0.254 0.314 -- 58.0
X Ray Diffraction 1.9474 2.0254 -- 152 1690 0.2111 0.3001 -- 80.0
X Ray Diffraction 2.0254 2.1176 -- 181 2013 0.1986 0.2461 -- 95.0
X Ray Diffraction 2.1176 2.2292 -- 182 2040 0.2036 0.2394 -- 95.0
X Ray Diffraction 2.2292 2.3689 -- 182 2036 0.2042 0.2373 -- 96.0
X Ray Diffraction 2.3689 2.5518 -- 186 2068 0.209 0.2493 -- 96.0
X Ray Diffraction 2.5518 2.8086 -- 189 2107 0.2128 0.2575 -- 97.0
X Ray Diffraction 2.8086 3.2149 -- 189 2109 0.2159 0.2406 -- 97.0
X Ray Diffraction 3.2149 4.0502 -- 197 2183 0.1731 0.2342 -- 98.0
X Ray Diffraction 4.0502 51.5024 -- 210 2349 0.189 0.2268 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.8
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_angle_d 1.068
f_dihedral_angle_d 13.371
f_bond_d 0.019
f_chiral_restr 0.065
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2193
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 223

Software

Software
Software Name Purpose
d*TREK data reduction version: 9.9.9.4 W9RSSI
PHENIX refinement version: 1.8.2_1309
PDB_EXTRACT data extraction version: 3.11
d*TREK data scaling