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_bond_d 0.011
f_angle_d 1.315
f_plane_restr 0.007
f_dihedral_angle_d 13.99
f_chiral_restr 0.099
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

Software
Software Name Purpose
PROTEUM PLUS data collection version: PLUS
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.1_743)
PROTEUM PLUS data reduction version: PLUS
PROTEUM PLUS data scaling version: PLUS