X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 298.0
Details 25% (v/v) polyethylene glycol 3,350, 0.15 M KSCN, 0.05 M NaCl, and 1:100 dilution of Hck-SH3-SH2-linker crystal seeds (grown in 25% v/v polyethylene glycol 3,350, 0.1 M Tris pH 8.5, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.71 α = 90
b = 60.71 β = 90
c = 49.58 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944 -- 2009-07-07
Diffraction Radiation
Monochromator Protocol
mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 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
2.61 50 98.2 0.056 -- -- 3.4 -- 6220 -- 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)
2.61 2.66 78.9 0.278 -- -- 2.3 270

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 2.61 25.89 -- 1.97 -- 5920 302 94.54 -- 0.1198 0.1194 0.1764 --
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 2.6061 3.2819 -- 142 2784 0.1738 0.2706 -- 89.0
X Ray Diffraction 3.2819 23.2277 -- 138 2828 0.0955 0.1402 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.0302
Anisotropic B[1][1] -1.4321
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.4321
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.3747
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.08
f_dihedral_angle_d 19.888
f_bond_d 0.007
f_angle_d 1.062
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1314
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 35

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHASER phasing
PHENIX refinement version: 1.6_289
PDB_EXTRACT data extraction version: 3.10
StructureStudio data collection
DENZO data reduction