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 = 79.01 α = 90
b = 79.01 β = 90
c = 107.53 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
2.3 70 100.0 -- 0.144 -- 34.6 -- 9312 -- -- --

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 2.3 68.426 -- 1.34 -- 9308 928 99.82 -- 0.2016 0.1967 0.2446 --
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 2.3 2.4214 -- 125 1156 0.2366 0.2912 -- 100.0
X Ray Diffraction 2.4214 2.5731 -- 130 1165 0.2261 0.2747 -- 100.0
X Ray Diffraction 2.5731 2.7717 -- 130 1172 0.2211 0.2937 -- 100.0
X Ray Diffraction 2.7717 3.0507 -- 131 1186 0.1964 0.2661 -- 100.0
X Ray Diffraction 3.0507 3.4921 -- 132 1178 0.1916 0.2504 -- 100.0
X Ray Diffraction 3.4921 4.3996 -- 134 1218 0.1723 0.1944 -- 99.0
X Ray Diffraction 4.3996 68.4567 -- 146 1305 0.1866 0.2256 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.2214
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.2214
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.4429
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.091
f_dihedral_angle_d 25.801
f_angle_d 1.225
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1322
Nucleic Acid Atoms 0
Heterogen Atoms 94
Solvent Atoms 143

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