X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 277.0
Details 8% PEG 4000, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.3 α = 90
b = 108.94 β = 90
c = 144.23 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 ADSC QUANTUM 315 Double Crystal 2010-11-24
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2

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
1.65 60 97.7 0.046 0.046 -- 3.8 110828 108279 -3.0 -3.0 25.627
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)
1.65 1.69 96.5 0.393 0.393 2.4 3.8 7826

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 1.65 37.092 -- 1.34 -- 108082 5418 97.26 -- 0.1774 0.1757 0.2103 --
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 1.65 1.6687 -- 184 3342 0.2736 0.2941 -- 96.0
X Ray Diffraction 1.6687 1.6884 -- 202 3302 0.2737 0.3442 -- 96.0
X Ray Diffraction 1.6884 1.709 -- 160 3363 0.2695 0.3225 -- 96.0
X Ray Diffraction 1.709 1.7306 -- 171 3365 0.2478 0.3093 -- 96.0
X Ray Diffraction 1.7306 1.7534 -- 217 3314 0.2466 0.2742 -- 96.0
X Ray Diffraction 1.7534 1.7774 -- 162 3367 0.2273 0.2721 -- 97.0
X Ray Diffraction 1.7774 1.8028 -- 173 3331 0.223 0.2521 -- 97.0
X Ray Diffraction 1.8028 1.8297 -- 194 3378 0.2102 0.2319 -- 97.0
X Ray Diffraction 1.8297 1.8583 -- 172 3363 0.2072 0.2711 -- 97.0
X Ray Diffraction 1.8583 1.8887 -- 163 3391 0.202 0.2497 -- 97.0
X Ray Diffraction 1.8887 1.9213 -- 174 3408 0.1937 0.2088 -- 97.0
X Ray Diffraction 1.9213 1.9562 -- 172 3367 0.1896 0.2381 -- 97.0
X Ray Diffraction 1.9562 1.9939 -- 192 3415 0.188 0.231 -- 97.0
X Ray Diffraction 1.9939 2.0346 -- 165 3365 0.1802 0.2636 -- 97.0
X Ray Diffraction 2.0346 2.0788 -- 180 3448 0.1769 0.194 -- 98.0
X Ray Diffraction 2.0788 2.1272 -- 185 3396 0.1778 0.2384 -- 97.0
X Ray Diffraction 2.1272 2.1803 -- 173 3426 0.1683 0.2303 -- 98.0
X Ray Diffraction 2.1803 2.2393 -- 204 3393 0.1646 0.1894 -- 98.0
X Ray Diffraction 2.2393 2.3052 -- 179 3432 0.1725 0.1981 -- 98.0
X Ray Diffraction 2.3052 2.3796 -- 169 3458 0.1682 0.2192 -- 98.0
X Ray Diffraction 2.3796 2.4646 -- 192 3445 0.174 0.2329 -- 98.0
X Ray Diffraction 2.4646 2.5633 -- 175 3452 0.1797 0.2156 -- 98.0
X Ray Diffraction 2.5633 2.6799 -- 177 3487 0.1708 0.2023 -- 98.0
X Ray Diffraction 2.6799 2.8211 -- 178 3470 0.1658 0.1991 -- 98.0
X Ray Diffraction 2.8211 2.9978 -- 181 3492 0.1648 0.1936 -- 99.0
X Ray Diffraction 2.9978 3.2291 -- 173 3537 0.1766 0.2094 -- 99.0
X Ray Diffraction 3.2291 3.5539 -- 171 3539 0.1764 0.2172 -- 99.0
X Ray Diffraction 3.5539 4.0676 -- 183 3558 0.1525 0.1875 -- 99.0
X Ray Diffraction 4.0676 5.1226 -- 182 3596 0.1435 0.1654 -- 99.0
X Ray Diffraction 5.1226 37.1012 -- 215 3464 0.1905 0.2058 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.261
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.6081
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.3471
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.099
f_dihedral_angle_d 13.99
f_angle_d 1.315
f_bond_d 0.011
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6179
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 787

Software

Computing
Computing Package Purpose
PROTEUM PLUS Data Collection
PROTEUM PLUS Data Reduction (intensity integration)
PROTEUM PLUS Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHASER model building
PROTEUM version: PLUS data collection