X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details 11% PEG 10000, 0.2 M magnesium acetate, 0.1 M MES, pH 6.5, Silver Bullet 33 (0.20% w/v D-(+)-Maltose monohydrate, 0.20% w/v D-(+)-Melibiose monohydrate, 0.20% w/v D-(+)-Raffinose pentahydrate, 0.20% w/v D-(+)-Trehalose dihydrate, 0.20% w/v Stachyose hydrate, 0.02 M HEPES sodium pH 6.8), Silver Bullet 70 (0.2% w/v Anthrone, 0.2% w/v Benzidine, 0.2% w/v N-(2-Acetamido)-2-aminoethanesulfonic acid, 0.2% w/v Phenylurea, 0.2% w/v -Alanine, 0.02 M HEPES sodium pH 6.8), VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 125.98 α = 90
b = 126.05 β = 93.17
c = 129.62 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-10-18
Diffraction Radiation
Monochromator Protocol
K-B pair of biomorph mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.979 APS 23-ID-D

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
3.4 19.87 99.2 -- 0.103 -- -- 55841 55419 0.0 -3.0 --
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)
3.4 3.5 99.9 -- -- 2.62 3.84 4626

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 3.4 19.819 -- 1.99 55841 55408 2894 99.78 -- 0.2325 0.2301 0.2773 thin shells
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 3.4 3.4555 -- 127 2443 0.2826 0.3361 -- 100.0
X Ray Diffraction 3.4555 3.5147 -- 140 2520 0.271 0.3386 -- 100.0
X Ray Diffraction 3.5147 3.5783 -- 141 2478 0.2709 0.3497 -- 100.0
X Ray Diffraction 3.5783 3.6467 -- 138 2463 0.265 0.3321 -- 100.0
X Ray Diffraction 3.6467 3.7207 -- 143 2540 0.2513 0.3314 -- 100.0
X Ray Diffraction 3.7207 3.801 -- 135 2491 0.2523 0.3051 -- 100.0
X Ray Diffraction 3.801 3.8888 -- 139 2461 0.2506 0.3209 -- 100.0
X Ray Diffraction 3.8888 3.9853 -- 140 2488 0.2421 0.3188 -- 100.0
X Ray Diffraction 3.9853 4.0921 -- 121 2530 0.2351 0.2866 -- 100.0
X Ray Diffraction 4.0921 4.2114 -- 122 2537 0.2206 0.2796 -- 100.0
X Ray Diffraction 4.2114 4.346 -- 156 2473 0.2076 0.259 -- 100.0
X Ray Diffraction 4.346 4.4995 -- 162 2472 0.1948 0.2351 -- 100.0
X Ray Diffraction 4.4995 4.6774 -- 128 2501 0.2032 0.2276 -- 100.0
X Ray Diffraction 4.6774 4.8873 -- 122 2509 0.2152 0.28 -- 100.0
X Ray Diffraction 4.8873 5.1407 -- 155 2474 0.2266 0.2841 -- 100.0
X Ray Diffraction 5.1407 5.4565 -- 156 2502 0.2452 0.2623 -- 100.0
X Ray Diffraction 5.4565 5.8676 -- 106 2521 0.279 0.3784 -- 100.0
X Ray Diffraction 5.8676 6.4396 -- 105 2553 0.2533 0.3246 -- 100.0
X Ray Diffraction 6.4396 7.3299 -- 152 2498 0.2438 0.2967 -- 100.0
X Ray Diffraction 7.3299 9.0844 -- 154 2517 0.1994 0.2343 -- 99.0
X Ray Diffraction 9.0844 19.8191 -- 152 2543 0.2092 0.2289 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -17.2636
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.748
Anisotropic B[2][2] -22.9013
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 40.1649
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.102
f_dihedral_angle_d 18.123
f_angle_d 1.449
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22720
Nucleic Acid Atoms 0
Heterogen Atoms 172
Solvent Atoms 0

Software

Computing
Computing Package Purpose
JBluIce Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHENIX AutoMR 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 version: AutoMR model building
JBluIce data collection