X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 291.0
Details 0.1 M Bis-Tris pH 6.5, 25% PEG 3,350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.47 α = 90
b = 90.55 β = 90
c = 132.97 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 PILATUS 2M -- 2014-11-03
Diffraction Radiation
Monochromator Protocol
Double Crystal Si111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.27050 ELETTRA 5.2R

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
2.1 48 99.8 0.117 -- -- 8.7 -- 36965 -- -- 29.44
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)
2.1 2.16 98.4 0.819 -- -- 8.3 --

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 2.103 48.0 -- 1.34 -- 36872 1858 99.73 -- 0.2113 0.2097 0.2398 --
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 2.1025 2.1594 -- 149 2602 0.2948 0.3528 0.0 98.0
X Ray Diffraction 2.1594 2.2229 -- 130 2650 0.2721 0.3187 0.0 100.0
X Ray Diffraction 2.2229 2.2947 -- 158 2643 0.271 0.3583 0.0 100.0
X Ray Diffraction 2.2947 2.3767 -- 132 2689 0.2497 0.2771 0.0 100.0
X Ray Diffraction 2.3767 2.4718 -- 143 2646 0.2566 0.3106 0.0 100.0
X Ray Diffraction 2.4718 2.5843 -- 133 2691 0.2479 0.2738 0.0 100.0
X Ray Diffraction 2.5843 2.7205 -- 144 2668 0.2428 0.296 0.0 100.0
X Ray Diffraction 2.7205 2.891 -- 117 2694 0.2384 0.2666 0.0 100.0
X Ray Diffraction 2.891 3.1142 -- 133 2701 0.2343 0.2906 0.0 100.0
X Ray Diffraction 3.1142 3.4275 -- 165 2691 0.2149 0.2738 0.0 100.0
X Ray Diffraction 3.4275 3.9232 -- 122 2738 0.1854 0.2459 0.0 100.0
X Ray Diffraction 3.9232 4.9421 -- 155 2734 0.157 0.1576 0.0 100.0
X Ray Diffraction 4.9421 48.0138 -- 177 2867 0.178 0.1804 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.3051
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_dihedral_angle_d 15.79
f_angle_d 0.448
f_chiral_restr 0.039
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4223
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 335

Software

Software
Software Name Purpose
XDS data reduction
Aimless data scaling version: 0.5.17
MOLREP phasing
PHENIX refinement
PDB_EXTRACT data extraction version: 3.22