X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 3.2 M sodium formate, 0.1 M Tris, pH 8.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.52 α = 90
b = 110.52 β = 90
c = 95.41 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 ADSC QUANTUM 315 -- 2013-08-01
Diffraction Radiation
Monochromator Protocol
single crystal Si(220) side bounce SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E

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
2.3 50 99.3 -- -- -- 11.9 -- 29872 -- -- --
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)
2.3 2.38 98.4 -- -- -- 10.4 --

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 2.305 47.818 -- 1.34 -- 29778 1513 98.9 -- 0.1857 0.1841 0.2135 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 2.3054 2.3798 -- 140 2458 0.2688 0.3123 -- 96.0
X Ray Diffraction 2.3798 2.4648 -- 140 2519 0.2409 0.2847 -- 98.0
X Ray Diffraction 2.4648 2.5635 -- 121 2572 0.2285 0.2974 -- 99.0
X Ray Diffraction 2.5635 2.6802 -- 131 2512 0.2176 0.2282 -- 99.0
X Ray Diffraction 2.6802 2.8214 -- 136 2555 0.21 0.3147 -- 99.0
X Ray Diffraction 2.8214 2.9982 -- 131 2541 0.1973 0.2153 -- 99.0
X Ray Diffraction 2.9982 3.2296 -- 158 2554 0.1869 0.2379 -- 100.0
X Ray Diffraction 3.2296 3.5546 -- 131 2614 0.1659 0.2131 -- 99.0
X Ray Diffraction 3.5546 4.0687 -- 149 2572 0.1583 0.2065 -- 100.0
X Ray Diffraction 4.0687 5.1252 -- 135 2631 0.1509 0.1696 -- 100.0
X Ray Diffraction 5.1252 47.8284 -- 141 2737 0.1964 0.184 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.254
f_dihedral_angle_d 16.165
f_chiral_restr 0.091
f_bond_d 0.008
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2960
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 124

Software

Software
Software Name Purpose
PHENIX refinement version: 1.8.2_1309
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing
Coot model building