X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 293.15
Details 50 mM MES pH 6.5, 12% PEG 400, 12 mM MnCl2, 100 mM NaCl, 10 mM EDTA, VAPOR DIFFUSION, temperature 293.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.51 α = 90
b = 105.51 β = 90
c = 488.23 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2013-05-25
Diffraction Radiation
Monochromator Protocol
don't know. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I24 0.96863 DIAMOND I24

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
3.2 30 90.0 -- -- -- -- 44335 44335 3.0 3.0 --

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
-- 3.306 19.997 -- 1.99 -- 44335 2217 97.51 -- 0.2405 0.2376 0.2946 --
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 3.3062 3.3777 -- 123 2371 0.4072 0.4257 -- 89.0
X Ray Diffraction 3.3777 3.4559 -- 140 2661 0.3667 0.4161 -- 99.0
X Ray Diffraction 3.4559 3.5419 -- 138 2616 0.3592 0.3957 -- 97.0
X Ray Diffraction 3.5419 3.6371 -- 140 2667 0.3292 0.3606 -- 98.0
X Ray Diffraction 3.6371 3.7434 -- 143 2659 0.3282 0.3624 -- 98.0
X Ray Diffraction 3.7434 3.8634 -- 140 2636 0.3209 0.3769 -- 99.0
X Ray Diffraction 3.8634 4.0004 -- 139 2669 0.2984 0.3905 -- 99.0
X Ray Diffraction 4.0004 4.1592 -- 139 2677 0.2824 0.3239 -- 99.0
X Ray Diffraction 4.1592 4.3467 -- 144 2663 0.2702 0.3352 -- 99.0
X Ray Diffraction 4.3467 4.5733 -- 139 2704 0.2438 0.3458 -- 99.0
X Ray Diffraction 4.5733 4.856 -- 140 2630 0.231 0.2792 -- 99.0
X Ray Diffraction 4.856 5.2247 -- 140 2682 0.2421 0.3229 -- 99.0
X Ray Diffraction 5.2247 5.7392 -- 137 2653 0.237 0.3176 -- 98.0
X Ray Diffraction 5.7392 6.544 -- 141 2663 0.2462 0.3206 -- 98.0
X Ray Diffraction 6.544 8.1508 -- 140 2620 0.2165 0.2518 -- 97.0
X Ray Diffraction 8.1508 19.9969 -- 134 2547 0.1419 0.1914 -- 94.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.093
f_dihedral_angle_d 28.492
f_angle_d 1.597
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9299
Nucleic Acid Atoms 5841
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.2_1309) refinement
PHASES model building