X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 17-24% PEG2000 MME, 100 mM Tris, pH 8.5, 100 mM triethylamine N-oxide

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.33 α = 90
b = 68.73 β = 90
c = 114.09 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- 2013-05-13
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2

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
2.24 50 94.4 -- 0.043 -- 3.1 -- 23132 -- -- 34.6484
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)
2.243 2.29 84.7 0.257 -- 1.47 2.5 --

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 2.24268 31.663 -- 1.38119 -- 23108 1198 94.2184 -- 0.187883 0.185411 0.232364 --
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 2.2427 2.3324 -- 120 2165 0.23795 0.281867 -- 85.1659
X Ray Diffraction 2.3324 2.4386 -- 128 2375 0.229717 0.272642 -- 93.0829
X Ray Diffraction 2.4386 2.5671 -- 133 2321 0.221877 0.281214 -- 92.4991
X Ray Diffraction 2.5671 2.7278 -- 125 2372 0.224437 0.319273 -- 92.3788
X Ray Diffraction 2.7278 2.9383 -- 127 2446 0.221185 0.258922 -- 95.6506
X Ray Diffraction 2.9383 3.2337 -- 161 2517 0.206031 0.235901 -- 98.6735
X Ray Diffraction 3.2337 3.701 -- 142 2551 0.186415 0.234577 -- 98.4284
X Ray Diffraction 3.701 4.6605 -- 132 2563 0.154803 0.202598 -- 97.5036
X Ray Diffraction 4.6605 31.6661 -- 130 2600 0.150719 0.188454 -- 94.3657
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.0198
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.00208712
f_angle_d 0.767382
f_dihedral_angle_d 14.0155
f_plane_restr 0.00312889
f_chiral_restr 0.0263395
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3915
Nucleic Acid Atoms 0
Heterogen Atoms 69
Solvent Atoms 179

Software

Software
Software Name Purpose
PHENIX refinement version: (phenix.refine: 1.8.4_1496)
PHASER phasing
PDB_EXTRACT data extraction version: 3.15
SCALA data scaling