X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6
Details 0.1 M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.4 α = 90
b = 93.4 β = 90
c = 362.04 γ = 90
Symmetry
Space Group P 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL (PILATUS) DECTRIS MIRRORS 2012-04-28
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I24 -- 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
2.5 30 99.9 0.11 -- -- 12.6 -- 56728 -- 3.0 46.53
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)
2.5 2.6 100.0 0.76 -- 3.25 11.7 --

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
OTHER 2.5 29.536 -- 2.01 -- 56672 2834 99.89 -- 0.2224 0.2202 0.2636 --
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 2.5 2.5431 -- 139 2640 0.3218 0.3718 -- 100.0
X Ray Diffraction 2.5431 2.5893 -- 140 2645 0.3096 0.4216 -- 100.0
X Ray Diffraction 2.5893 2.6391 -- 138 2628 0.297 0.3792 -- 100.0
X Ray Diffraction 2.6391 2.6929 -- 139 2648 0.281 0.3281 -- 100.0
X Ray Diffraction 2.6929 2.7514 -- 142 2685 0.2602 0.3333 -- 100.0
X Ray Diffraction 2.7514 2.8154 -- 137 2611 0.2525 0.2825 -- 100.0
X Ray Diffraction 2.8154 2.8857 -- 139 2645 0.2516 0.3419 -- 100.0
X Ray Diffraction 2.8857 2.9637 -- 139 2630 0.2371 0.3066 -- 100.0
X Ray Diffraction 2.9637 3.0508 -- 141 2674 0.243 0.3082 -- 100.0
X Ray Diffraction 3.0508 3.1492 -- 140 2673 0.2436 0.2773 -- 100.0
X Ray Diffraction 3.1492 3.2616 -- 141 2670 0.2328 0.2686 -- 100.0
X Ray Diffraction 3.2616 3.392 -- 140 2659 0.2361 0.3293 -- 100.0
X Ray Diffraction 3.392 3.5461 -- 141 2688 0.2303 0.2653 -- 100.0
X Ray Diffraction 3.5461 3.7327 -- 142 2706 0.224 0.2748 -- 100.0
X Ray Diffraction 3.7327 3.9661 -- 141 2679 0.2084 0.2263 -- 100.0
X Ray Diffraction 3.9661 4.2715 -- 144 2730 0.1847 0.2323 -- 100.0
X Ray Diffraction 4.2715 4.6998 -- 143 2725 0.1625 0.2016 -- 100.0
X Ray Diffraction 4.6998 5.3763 -- 145 2748 0.1848 0.2219 -- 100.0
X Ray Diffraction 5.3763 6.7602 -- 148 2807 0.2376 0.2646 -- 100.0
X Ray Diffraction 6.7602 29.5377 -- 155 2947 0.2054 0.2205 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 13.6276
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 13.6276
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.2148
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.044
f_dihedral_angle_d 12.604
f_angle_d 0.634
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10389
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 289

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (PHENIX.REFINE: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE: 1.7.3_928) refinement
PHENIX model building