X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.6
Temperature 293.0
Details 20 mM HEPES, 10% PEG 2000, 20 mM Cobalt(III) Hexammine Choride, 1 mM C10E8, pH 7.6, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 172.35 α = 90
b = 182.86 β = 90
c = 430.39 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2009-01-01
CCD MARMOSAIC 325 mm CCD -- 2009-01-01
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal SINGLE WAVELENGTH
Liquid nitrogen-cooled double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 1.00 SSRL BL12-2
SYNCHROTRON SSRL BEAMLINE BL12-2 1.25499, 1.25462, 1.03317 SSRL BL12-2

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
2.88 100 98.9 0.096 -- -- 4.6 -- 299154 -- -- 66.7
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)
2.88 3.0 96.3 0.505 -- -- 4.3 28859

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
MAD 2.88 43.956 -- 0.1 -- 275516 13889 90.75 -- 0.2192 0.2176 0.2486 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 2.88 2.9201 -- 307 6193 0.3161 0.341 -- 65.0
X Ray Diffraction 2.9201 2.9545 -- 395 7469 0.3001 0.3512 -- 78.0
X Ray Diffraction 2.9545 2.9905 -- 430 7694 0.3057 0.3674 -- 81.0
X Ray Diffraction 2.9905 3.0283 -- 435 7764 0.2946 0.3378 -- 81.0
X Ray Diffraction 3.0283 3.0682 -- 436 7912 0.2884 0.3269 -- 84.0
X Ray Diffraction 3.0682 3.1102 -- 452 8077 0.278 0.3436 -- 85.0
X Ray Diffraction 3.1102 3.1546 -- 457 8135 0.2843 0.33 -- 85.0
X Ray Diffraction 3.1546 3.2017 -- 430 8264 0.2756 0.3142 -- 87.0
X Ray Diffraction 3.2017 3.2517 -- 438 8401 0.2628 0.3119 -- 88.0
X Ray Diffraction 3.2517 3.305 -- 453 8532 0.2685 0.2987 -- 89.0
X Ray Diffraction 3.305 3.3619 -- 457 8436 0.2589 0.3087 -- 89.0
X Ray Diffraction 3.3619 3.4231 -- 438 8605 0.2528 0.3048 -- 90.0
X Ray Diffraction 3.4231 3.4889 -- 465 8759 0.2513 0.2874 -- 91.0
X Ray Diffraction 3.4889 3.5601 -- 495 8754 0.2351 0.2653 -- 92.0
X Ray Diffraction 3.5601 3.6374 -- 488 8906 0.2354 0.2807 -- 93.0
X Ray Diffraction 3.6374 3.722 -- 469 8987 0.2279 0.2685 -- 94.0
X Ray Diffraction 3.722 3.815 -- 496 9012 0.2172 0.2641 -- 94.0
X Ray Diffraction 3.815 3.9181 -- 453 9021 0.2139 0.2306 -- 94.0
X Ray Diffraction 3.9181 4.0333 -- 504 9109 0.1994 0.23 -- 95.0
X Ray Diffraction 4.0333 4.1634 -- 510 9114 0.1985 0.2342 -- 95.0
X Ray Diffraction 4.1634 4.3121 -- 455 9280 0.1801 0.215 -- 96.0
X Ray Diffraction 4.3121 4.4846 -- 483 9339 0.1714 0.1933 -- 97.0
X Ray Diffraction 4.4846 4.6885 -- 492 9357 0.1627 0.183 -- 97.0
X Ray Diffraction 4.6885 4.9354 -- 511 9372 0.1591 0.1815 -- 97.0
X Ray Diffraction 4.9354 5.2441 -- 493 9444 0.1598 0.1749 -- 98.0
X Ray Diffraction 5.2441 5.6482 -- 453 9474 0.1763 0.2109 -- 98.0
X Ray Diffraction 5.6482 6.2152 -- 509 9465 0.1847 0.2159 -- 97.0
X Ray Diffraction 6.2152 7.1113 -- 487 9532 0.1992 0.226 -- 97.0
X Ray Diffraction 7.1113 8.9471 -- 484 9598 0.1785 0.205 -- 97.0
X Ray Diffraction 8.9471 43.9609 -- 514 9622 0.2201 0.2184 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.2557
Anisotropic B[1][1] 9.461
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 14.9775
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -24.4384
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.078
f_plane_restr 0.004
f_chiral_restr 0.068
f_angle_d 1.053
f_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4156
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 62298
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 650

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHELXD Structure Solution
PHENIX (phenix.refine: 1.5_2) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SHELX phasing
SCALEPACK data scaling
DENZO reflection data processing