X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Details VAPOUR DIFFUSION(1:1): 17 % PEG 3350, 0.02 M NAK PHOSPHATE, 0.1 M BIS-TRIS PROPANE PH 8.0, 1 MM TCEP 15 MG/ML PROTEIN

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.74 α = 87.46
b = 93.9 β = 80.45
c = 162.81 γ = 68.33
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 -- 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
1.95 34 94.0 0.09 -- -- 2.9 -- 359608 -- 2.0 16.33
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)
1.95 2.0 80.0 0.44 -- 2.38 2.7 --

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
MOLECULAR REPLACEMENT 1.95 33.936 -- 1.99 -- 351605 17580 94.82 -- 0.1958 0.1925 0.2573 --
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 1.95 2.0197 -- 1550 29444 0.2299 0.3193 -- 84.0
X Ray Diffraction 2.0197 2.1005 -- 1772 33672 0.2127 0.2995 -- 95.0
X Ray Diffraction 2.1005 2.1961 -- 1782 33854 0.2007 0.2899 -- 96.0
X Ray Diffraction 2.1961 2.3119 -- 1759 33425 0.1972 0.2847 -- 95.0
X Ray Diffraction 2.3119 2.4567 -- 1795 34114 0.193 0.2863 -- 97.0
X Ray Diffraction 2.4567 2.6463 -- 1791 34026 0.1875 0.2704 -- 97.0
X Ray Diffraction 2.6463 2.9125 -- 1800 34201 0.1905 0.268 -- 97.0
X Ray Diffraction 2.9125 3.3336 -- 1794 34078 0.1868 0.2448 -- 97.0
X Ray Diffraction 3.3336 4.1988 -- 1777 33767 0.182 0.2274 -- 96.0
X Ray Diffraction 4.1988 33.9409 -- 1760 33444 0.1896 0.2208 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.431
Anisotropic B[1][2] 0.5355
Anisotropic B[1][3] 0.7097
Anisotropic B[2][2] 1.5511
Anisotropic B[2][3] 5.0E-4
Anisotropic B[3][3] 1.2577
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_bond_d 0.009
f_dihedral_angle_d 14.053
f_chiral_restr 0.076
f_angle_d 1.109
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 39464
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 5676

Software

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
XSCALE data scaling
PHASER phasing