X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 50 mM Tris, 1.9 M cesium chloride, 50% DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.6 α = 90
b = 92.6 β = 90
c = 130.4 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 Collimating Mirror 2010-06-25
Diffraction Radiation
Monochromator Protocol
Double Crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

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
1.66 50 99.7 -- 0.054 -- 5.5 39580 39580 -- -- --
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)
1.66 1.69 99.7 -- 0.22 7.6 5.4 1938

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 1.66 43.631 -- 0.0 40654 38705 1949 97.64 0.1405 0.1405 0.1391 0.1658 RANDOM
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 1.6601 1.7016 -- 155 2467 0.1655 0.2109 -- 94.0
X Ray Diffraction 1.7016 1.7476 -- 128 2519 0.1573 0.1969 -- 95.0
X Ray Diffraction 1.7476 1.799 -- 114 2550 0.1431 0.1798 -- 96.0
X Ray Diffraction 1.799 1.8571 -- 155 2534 0.1327 0.1919 -- 96.0
X Ray Diffraction 1.8571 1.9235 -- 154 2539 0.1332 0.1874 -- 97.0
X Ray Diffraction 1.9235 2.0005 -- 132 2576 0.1299 0.1903 -- 98.0
X Ray Diffraction 2.0005 2.0915 -- 129 2626 0.1304 0.1473 -- 99.0
X Ray Diffraction 2.0915 2.2018 -- 150 2625 0.1243 0.161 -- 99.0
X Ray Diffraction 2.2018 2.3397 -- 121 2650 0.1289 0.1412 -- 99.0
X Ray Diffraction 2.3397 2.5204 -- 137 2665 0.1333 0.1568 -- 99.0
X Ray Diffraction 2.5204 2.774 -- 137 2668 0.1367 0.1754 -- 99.0
X Ray Diffraction 2.774 3.1753 -- 133 2712 0.1343 0.1429 -- 99.0
X Ray Diffraction 3.1753 4.0001 -- 155 2751 0.1377 0.1511 -- 100.0
X Ray Diffraction 4.0001 43.6464 -- 149 2874 0.159 0.1714 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.2182
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.2182
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.4365
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.074
f_dihedral_angle_d 13.124
f_angle_d 1.03
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2428
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 432

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
PHASER model building
MAR345dtb data collection