X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
Temperature 298.0
Details 35% 5/4 PO/OH, 50 mM Hepes, 300 mM NaCl, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 148.49 α = 90
b = 148.49 β = 90
c = 129.67 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-11-17
Diffraction Radiation
Monochromator Protocol
Double flat crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.11589 ALS 8.3.1

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 48.85 -- -- -- -- -- 108207 104042 -- -- --

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
-- 2.5 48.836 -- 1.97 -- 100721 5413 91.05 -- 0.1984 0.1969 0.2316 --
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 2.5431 -- 241 4467 0.2665 0.3056 -- 82.0
X Ray Diffraction 2.5431 2.5894 -- 256 4581 0.2577 0.2794 -- 82.0
X Ray Diffraction 2.5894 2.6392 -- 262 4526 0.2591 0.2956 -- 82.0
X Ray Diffraction 2.6392 2.693 -- 230 4628 0.2506 0.2789 -- 83.0
X Ray Diffraction 2.693 2.7516 -- 264 4577 0.2323 0.252 -- 83.0
X Ray Diffraction 2.7516 2.8156 -- 223 4697 0.2396 0.2673 -- 85.0
X Ray Diffraction 2.8156 2.886 -- 275 4571 0.2371 0.2714 -- 83.0
X Ray Diffraction 2.886 2.964 -- 220 4695 0.2336 0.2756 -- 85.0
X Ray Diffraction 2.964 3.0512 -- 247 4689 0.2269 0.2952 -- 85.0
X Ray Diffraction 3.0512 3.1497 -- 242 4766 0.2211 0.2421 -- 86.0
X Ray Diffraction 3.1497 3.2622 -- 252 4694 0.2101 0.291 -- 85.0
X Ray Diffraction 3.2622 3.3928 -- 240 4829 0.1922 0.2359 -- 86.0
X Ray Diffraction 3.3928 3.5471 -- 245 4823 0.191 0.2432 -- 88.0
X Ray Diffraction 3.5471 3.7341 -- 227 4970 0.1756 0.2105 -- 89.0
X Ray Diffraction 3.7341 3.9679 -- 259 4973 0.1734 0.2049 -- 90.0
X Ray Diffraction 3.9679 4.2741 -- 250 5027 0.1609 0.192 -- 91.0
X Ray Diffraction 4.2741 4.7038 -- 291 4991 0.1543 0.179 -- 90.0
X Ray Diffraction 4.7038 5.3835 -- 281 4998 0.1629 0.1947 -- 91.0
X Ray Diffraction 5.3835 6.779 -- 269 5165 0.1964 0.2457 -- 93.0
X Ray Diffraction 6.779 45.5201 -- 264 5011 0.1778 0.1898 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 3.2748
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.2748
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.5497
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.745
f_angle_d 1.249
f_plane_restr 0.006
f_chiral_restr 0.077
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 17189
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 19

Software

Software
Software Name Purpose
PHENIX refinement version: 1.7.1_743
PDB_EXTRACT data extraction version: 3.10