X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details 3.1M ammonium sulfate, 100mM citrate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 242.14 α = 90
b = 242.14 β = 90
c = 109.72 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2014-08-07
Diffraction Radiation
Monochromator Protocol
CRYO-COOLED SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C

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
2.23 39.91 96.0 0.026 -- -- 3.4 193355 57205 -- -- --
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)
2.23 2.29 92.0 0.85 -- 1.2 2.5 --

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 2.29 39.907 -- 1.34 -- 50642 2554 91.84 -- 0.2177 0.2171 0.2285 Derived from 3CAP, extended to higher resolution
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 2.29 2.3341 -- 117 2346 0.3672 0.3405 -- 81.0
X Ray Diffraction 2.3341 2.3817 -- 131 2577 0.3386 0.3425 -- 89.0
X Ray Diffraction 2.3817 2.4335 -- 146 2587 0.3369 0.3743 -- 90.0
X Ray Diffraction 2.4335 2.4901 -- 137 2603 0.3164 0.3474 -- 90.0
X Ray Diffraction 2.4901 2.5524 -- 155 2574 0.2815 0.2726 -- 90.0
X Ray Diffraction 2.5524 2.6214 -- 121 2607 0.278 0.2908 -- 90.0
X Ray Diffraction 2.6214 2.6985 -- 114 2613 0.2852 0.3164 -- 89.0
X Ray Diffraction 2.6985 2.7856 -- 135 2496 0.2629 0.3427 -- 86.0
X Ray Diffraction 2.7856 2.8851 -- 125 2515 0.237 0.2729 -- 85.0
X Ray Diffraction 2.8851 3.0006 -- 139 2703 0.2262 0.2713 -- 94.0
X Ray Diffraction 3.0006 3.1371 -- 158 2745 0.2213 0.2493 -- 95.0
X Ray Diffraction 3.1371 3.3024 -- 142 2775 0.2157 0.2432 -- 96.0
X Ray Diffraction 3.3024 3.5092 -- 179 2766 0.2167 0.2288 -- 96.0
X Ray Diffraction 3.5092 3.7799 -- 153 2697 0.1941 0.2112 -- 93.0
X Ray Diffraction 3.7799 4.16 -- 155 2857 0.1908 0.1944 -- 98.0
X Ray Diffraction 4.16 4.7611 -- 158 2884 0.1878 0.187 -- 99.0
X Ray Diffraction 4.7611 5.9952 -- 143 2882 0.1877 0.2039 -- 98.0
X Ray Diffraction 5.9952 39.9135 -- 146 2861 0.1945 0.1799 -- 95.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.004
f_plane_restr 0.004
f_angle_d 0.878
f_dihedral_angle_d 13.42
f_chiral_restr 0.036
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2677
Nucleic Acid Atoms 0
Heterogen Atoms 144
Solvent Atoms 65

Software

Software
Software Name Purpose
PHENIX refinement version: (phenix.refine: dev_1839)
XDS data scaling
Aimless data scaling
PHASER phasing