X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 15-20% PEG 6000, 0.15M NaOAc, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.92 α = 90
b = 78.92 β = 90
c = 106.18 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER SMART 6000 -- 2012-02-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 1.54 -- --

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 70 100.0 -- 0.16 -- 36.0 -- 7223 -- -- --

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
PDB entry 3M08 2.5 68.348 -- 1.34 -- 7218 723 99.94 -- 0.1972 0.1916 0.2463 --
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 2.6932 -- 140 1257 0.2242 0.3037 -- 100.0
X Ray Diffraction 2.6932 2.9643 -- 136 1265 0.2171 0.2629 -- 100.0
X Ray Diffraction 2.9643 3.3932 -- 147 1275 0.1974 0.2764 -- 100.0
X Ray Diffraction 3.3932 4.275 -- 146 1299 0.1767 0.2318 -- 100.0
X Ray Diffraction 4.275 68.3731 -- 154 1399 0.1776 0.2123 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -4.9774
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.9774
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.9548
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.087
f_dihedral_angle_d 23.655
f_angle_d 1.184
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1316
Nucleic Acid Atoms 0
Heterogen Atoms 93
Solvent Atoms 69

Software

Computing
Computing Package Purpose
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.2_869) refinement