X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 295.7
Details 11% PEG4000, 0.1 M Tris, pH 8.5 and 0.1 M MgCl2, vapor diffusion, sitting drop, temperature 295.7K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.62 α = 90
b = 136.62 β = 90
c = 142.13 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-03-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B

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
3 50 94.7 0.097 -- -- 3.9 -- 29412 -- -- --
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)
3.0 3.11 64.8 0.589 -- -- 3.2 1988

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 3.004 44.718 -- 0.0 -- 27264 1395 87.78 -- 0.2318 0.229 0.2822 --
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 3.0044 3.1117 -- 62 1476 0.368 0.3948 -- 50.0
X Ray Diffraction 3.1117 3.2363 -- 110 2082 0.3397 0.3997 -- 72.0
X Ray Diffraction 3.2363 3.3835 -- 125 2406 0.2984 0.3678 -- 82.0
X Ray Diffraction 3.3835 3.5618 -- 143 2566 0.2795 0.3449 -- 89.0
X Ray Diffraction 3.5618 3.7849 -- 149 2736 0.2498 0.3221 -- 94.0
X Ray Diffraction 3.7849 4.077 -- 156 2789 0.2157 0.2517 -- 96.0
X Ray Diffraction 4.077 4.4869 -- 169 2851 0.1857 0.2314 -- 97.0
X Ray Diffraction 4.4869 5.1353 -- 180 2902 0.1847 0.2585 -- 98.0
X Ray Diffraction 5.1353 6.4669 -- 146 2963 0.211 0.288 -- 99.0
X Ray Diffraction 6.4669 44.7227 -- 155 3098 0.2297 0.2656 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 98.2333
Anisotropic B[1][1] 6.5736
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.5736
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -13.1472
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_angle_d 1.229
f_chiral_restr 0.076
f_dihedral_angle_d 22.077
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6561
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
PHENIX refinement version: 1.7_650
PDB_EXTRACT data extraction version: 3.11