X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 292.15
Details 3 M NaCl, 0.1 M Bis-tris pH 5.5, 5 mM MgCl2, 5 mM beta-mercapto ethanol, 25% glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.29 α = 90
b = 86.29 β = 90
c = 113.82 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2015-04-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-3 0.972 MAX II I911-3

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
1.6 37.4 100.0 -- 0.14 -- 23.2 -- 125126 -- -- 16.4
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)
1.6 1.64 100.0 -- -- 1.7 22.8 --

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 1.6 37.4 -- 0.0 -- 63905 1975 98.09 -- 0.1582 0.1579 0.1681 Random selection
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 1.6 1.64 -- 138 4194 0.2532 0.2298 -- 94.0
X Ray Diffraction 1.64 1.6844 -- 129 4205 0.2328 0.2365 -- 95.0
X Ray Diffraction 1.6844 1.7339 -- 136 4263 0.2191 0.255 -- 95.0
X Ray Diffraction 1.7339 1.7899 -- 137 4304 0.2045 0.2151 -- 96.0
X Ray Diffraction 1.7899 1.8539 -- 139 4330 0.184 0.2178 -- 97.0
X Ray Diffraction 1.8539 1.9281 -- 138 4406 0.1698 0.2122 -- 98.0
X Ray Diffraction 1.9281 2.0158 -- 144 4437 0.1528 0.1684 -- 99.0
X Ray Diffraction 2.0158 2.1221 -- 144 4440 0.146 0.1502 -- 99.0
X Ray Diffraction 2.1221 2.255 -- 139 4485 0.1444 0.1469 -- 100.0
X Ray Diffraction 2.255 2.4291 -- 145 4492 0.1369 0.1484 -- 100.0
X Ray Diffraction 2.4291 2.6735 -- 146 4499 0.1489 0.1617 -- 100.0
X Ray Diffraction 2.6735 3.0602 -- 143 4534 0.1545 0.1702 -- 100.0
X Ray Diffraction 3.0602 3.8549 -- 145 4595 0.1416 0.1432 -- 100.0
X Ray Diffraction 3.8549 37.3748 -- 152 4746 0.151 0.1591 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.21
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.243
f_bond_d 0.014
f_angle_d 1.134
f_chiral_restr 0.171
f_plane_restr 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3113
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 352

Software

Software
Software Name Purpose
PHENIX refinement version: (1.10_2152: ???)
XDS data reduction
XSCALE data scaling
PHASER phasing
PHENIX model building