X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 295.0
Details 30% PEG 400,100mM Potassium Chloride, 10mM Magnesium Chloride, 50mM Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.06 α = 90
b = 64.06 β = 90
c = 183.89 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD beryllium lens 2009-07-31
Diffraction Radiation
Monochromator Protocol
C(111) diamond laue monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
1.9 50 99.9 0.088 -- -- 6.5 66749 66682 1.6 2.6 26.5
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)
1.9 1.97 100.0 0.663 -- 2.6 5.2 6704

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
SAD 1.9 32.03 2.6 1.44 66724 66598 3345 99.81 0.159 0.159 0.1572 0.1931 random
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 1.8982 1.966 6613 325 6288 0.2122 0.2947 -- 99.0
X Ray Diffraction 1.966 2.0447 6654 321 6333 0.1656 0.2076 -- 99.9
X Ray Diffraction 2.0447 2.1378 6727 318 6409 0.1481 0.17 -- 99.9
X Ray Diffraction 2.1378 2.2505 6585 335 6250 0.1457 0.2135 -- 100.0
X Ray Diffraction 2.2505 2.3914 6689 362 6326 0.1454 0.1917 -- 100.0
X Ray Diffraction 2.3914 2.576 6704 318 6386 0.145 0.1948 -- 99.9
X Ray Diffraction 2.576 2.8351 6644 341 6303 0.1476 0.205 -- 100.0
X Ray Diffraction 2.8351 3.245 6684 363 6321 0.146 0.1803 -- 99.9
X Ray Diffraction 3.245 4.087 6643 375 6268 0.145 0.1864 -- 99.9
X Ray Diffraction 4.087 32.0345 6659 287 6369 0.1774 0.1849 -- 99.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.2501
Anisotropic B[1][1] 5.6875
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.6875
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.353
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.607
f_chiral_restr 0.067
f_bond_d 0.007
f_angle_d 0.978
f_plane_restr 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3603
Nucleic Acid Atoms 0
Heterogen Atoms 110
Solvent Atoms 220

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: dev_501
PDB_EXTRACT data extraction version: 3.10
BLU-MAX data collection
HKL-2000 data reduction
HKL-2000 data scaling
SHELXS phasing