X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 0.2 M Lithium sulfate, 20% PEG 3350 and 0.1 M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.8 α = 90
b = 116.1 β = 90
c = 130 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2011-05-19
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.9219, 0.9794, 0.9793 SSRL BL9-2

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
2.29 50 99.6 0.062 -- -- 4.4 -- 50161 2.0 2.0 --
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)
2.29 2.33 99.7 0.619 -- -- 3.0 2689

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
MAD 2.29 34.56 -- 0.0 -- 45220 3951 89.42 -- 0.2513 0.2484 0.2807 --
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 2.3179 -- 108 1175 0.4348 0.4604 -- 68.0
X Ray Diffraction 2.3179 2.3473 -- 110 1200 0.4443 0.4977 -- 74.0
X Ray Diffraction 2.3473 2.3782 -- 125 1271 0.4157 0.4161 -- 77.0
X Ray Diffraction 2.3782 2.4107 -- 122 1287 0.4355 0.4054 -- 78.0
X Ray Diffraction 2.4107 2.4452 -- 122 1264 0.4091 0.4168 -- 78.0
X Ray Diffraction 2.4452 2.4817 -- 116 1291 0.3728 0.4042 -- 78.0
X Ray Diffraction 2.4817 2.5204 -- 131 1371 0.4195 0.3689 -- 84.0
X Ray Diffraction 2.5204 2.5617 -- 120 1360 0.367 0.3713 -- 81.0
X Ray Diffraction 2.5617 2.6059 -- 127 1356 0.3775 0.4716 -- 83.0
X Ray Diffraction 2.6059 2.6533 -- 138 1395 0.3863 0.4963 -- 85.0
X Ray Diffraction 2.6533 2.7043 -- 137 1379 0.3612 0.3554 -- 85.0
X Ray Diffraction 2.7043 2.7594 -- 148 1432 0.3613 0.3035 -- 86.0
X Ray Diffraction 2.7594 2.8194 -- 133 1489 0.3578 0.4337 -- 90.0
X Ray Diffraction 2.8194 2.885 -- 136 1511 0.3551 0.3576 -- 91.0
X Ray Diffraction 2.885 2.9571 -- 152 1519 0.3285 0.3429 -- 92.0
X Ray Diffraction 2.9571 3.037 -- 146 1557 0.3251 0.2887 -- 95.0
X Ray Diffraction 3.037 3.1263 -- 152 1584 0.3364 0.3789 -- 96.0
X Ray Diffraction 3.1263 3.2271 -- 159 1615 0.3275 0.4468 -- 98.0
X Ray Diffraction 3.2271 3.3424 -- 152 1625 0.2986 0.3408 -- 98.0
X Ray Diffraction 3.3424 3.4761 -- 156 1609 0.2799 0.3375 -- 99.0
X Ray Diffraction 3.4761 3.6341 -- 160 1613 0.2534 0.2469 -- 98.0
X Ray Diffraction 3.6341 3.8255 -- 156 1609 0.2428 0.3013 -- 99.0
X Ray Diffraction 3.8255 4.0648 -- 162 1660 0.2273 0.2619 -- 99.0
X Ray Diffraction 4.0648 4.3781 -- 161 1616 0.1872 0.2482 -- 99.0
X Ray Diffraction 4.3781 4.8177 -- 160 1638 0.174 0.1884 -- 100.0
X Ray Diffraction 4.8177 5.5124 -- 152 1651 0.1896 0.1882 -- 100.0
X Ray Diffraction 5.5124 6.9358 -- 156 1654 0.2162 0.2445 -- 100.0
X Ray Diffraction 6.9358 34.5641 -- 154 1538 0.1832 0.2517 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 105.056
Anisotropic B[1][1] 47.6199
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -27.4242
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -20.1957
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.263
f_plane_restr 0.004
f_chiral_restr 0.044
f_angle_d 0.656
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3273
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 56

Software

Computing
Computing Package Purpose
Webice Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction