X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 293.0
Details 50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 155.25 α = 90
b = 159.91 β = 90
c = 268.93 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2015-10-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU

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
3 49.55 99.9 0.11 -- -- 6.733 -- 134084 -- -3.0 84.07
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)
3.0 3.08 99.9 1.289 -- 1.52 6.4 --

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 3.0 49.552 -- 0.98 -- 134077 2987 99.89 -- 0.1956 0.1953 0.2253 --
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 3.0 3.0491 -- 125 12213 0.3344 0.3688 0.0 100.0
X Ray Diffraction 3.0491 3.1017 -- 146 12128 0.3207 0.3318 0.0 100.0
X Ray Diffraction 3.1017 3.1581 -- 147 12220 0.2981 0.3197 0.0 100.0
X Ray Diffraction 3.1581 3.2188 -- 135 12101 0.2706 0.2832 0.0 100.0
X Ray Diffraction 3.2188 3.2845 -- 141 12228 0.2628 0.2782 0.0 100.0
X Ray Diffraction 3.2845 3.3559 -- 141 12189 0.2646 0.2948 0.0 100.0
X Ray Diffraction 3.3559 3.434 -- 145 12137 0.2635 0.2987 0.0 100.0
X Ray Diffraction 3.434 3.5198 -- 151 12182 0.2446 0.2681 0.0 100.0
X Ray Diffraction 3.5198 3.615 -- 140 12202 0.23 0.2049 0.0 100.0
X Ray Diffraction 3.615 3.7213 -- 142 12195 0.2177 0.2882 0.0 100.0
X Ray Diffraction 3.7213 3.8414 -- 141 12209 0.2113 0.258 0.0 100.0
X Ray Diffraction 3.8414 3.9786 -- 153 12167 0.2019 0.2388 0.0 100.0
X Ray Diffraction 3.9786 4.1378 -- 141 12136 0.184 0.2239 0.0 100.0
X Ray Diffraction 4.1378 4.326 -- 142 12201 0.1639 0.1804 0.0 100.0
X Ray Diffraction 4.326 4.554 -- 144 12152 0.1573 0.2216 0.0 100.0
X Ray Diffraction 4.554 4.8391 -- 143 12197 0.1534 0.153 0.0 100.0
X Ray Diffraction 4.8391 5.2123 -- 136 12140 0.1665 0.2156 0.0 100.0
X Ray Diffraction 5.2123 5.7362 -- 150 12209 0.1783 0.2001 0.0 100.0
X Ray Diffraction 5.7362 6.5646 -- 132 12159 0.1887 0.2337 0.0 100.0
X Ray Diffraction 6.5646 8.2644 -- 148 12162 0.1713 0.215 0.0 100.0
X Ray Diffraction 8.2644 49.5587 -- 144 12146 0.1667 0.1836 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 92.111
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.005
f_plane_restr 0.006
f_chiral_restr 0.055
f_dihedral_angle_d 13.66
f_angle_d 0.889
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 32352
Nucleic Acid Atoms 1319
Heterogen Atoms 41
Solvent Atoms 0

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: 1.10.1_2155
PDB_EXTRACT data extraction version: 3.22
XDS data reduction
PHENIX phasing