X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 200 mM ammonium sulfate, 18% PEG 4000, 200 mM HEPES pH 7.0, 5% 2-METHYL-2,4-PENTANEDIOL, 0.5 mM beta-octyl glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.62 α = 90
b = 127.33 β = 90.25
c = 129.6 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2012-03-16
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.1271 APS 21-ID-D

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
3.05 30 99.9 0.131 -- -- 5.8 57781 57775 0.0 0.0 --
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)
3.05 3.16 100.0 0.706 -- 2.2 5.9 5717

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 3.05 29.775 -- 1.34 57781 57732 5877 99.5 -- 0.1829 0.1758 0.2452 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 3.05 3.0725 -- 165 1497 0.2846 0.3477 -- 86.0
X Ray Diffraction 3.0725 3.1086 -- 215 1665 0.2664 0.3484 -- 100.0
X Ray Diffraction 3.1086 3.1465 -- 196 1759 0.2671 0.3462 -- 100.0
X Ray Diffraction 3.1465 3.1863 -- 218 1745 0.2629 0.3585 -- 100.0
X Ray Diffraction 3.1863 3.2281 -- 195 1684 0.2586 0.3222 -- 100.0
X Ray Diffraction 3.2281 3.2723 -- 201 1727 0.2578 0.3462 -- 100.0
X Ray Diffraction 3.2723 3.319 -- 183 1754 0.2561 0.3628 -- 100.0
X Ray Diffraction 3.319 3.3685 -- 181 1729 0.2574 0.3346 -- 100.0
X Ray Diffraction 3.3685 3.421 -- 212 1734 0.2242 0.3257 -- 100.0
X Ray Diffraction 3.421 3.477 -- 184 1715 0.213 0.2812 -- 100.0
X Ray Diffraction 3.477 3.5369 -- 196 1737 0.2019 0.2656 -- 100.0
X Ray Diffraction 3.5369 3.6011 -- 183 1738 0.1912 0.2778 -- 100.0
X Ray Diffraction 3.6011 3.6702 -- 194 1714 0.1831 0.2781 -- 100.0
X Ray Diffraction 3.6702 3.745 -- 231 1717 0.1698 0.2391 -- 100.0
X Ray Diffraction 3.745 3.8263 -- 206 1731 0.1638 0.2304 -- 100.0
X Ray Diffraction 3.8263 3.9151 -- 186 1739 0.1576 0.24 -- 100.0
X Ray Diffraction 3.9151 4.0128 -- 199 1731 0.153 0.2324 -- 100.0
X Ray Diffraction 4.0128 4.121 -- 201 1727 0.162 0.2328 -- 100.0
X Ray Diffraction 4.121 4.242 -- 187 1759 0.1633 0.2426 -- 100.0
X Ray Diffraction 4.242 4.3785 -- 184 1728 0.1545 0.2406 -- 100.0
X Ray Diffraction 4.3785 4.5344 -- 185 1775 0.1528 0.2104 -- 100.0
X Ray Diffraction 4.5344 4.7153 -- 207 1706 0.1446 0.1821 -- 100.0
X Ray Diffraction 4.7153 4.929 -- 192 1761 0.143 0.2071 -- 100.0
X Ray Diffraction 4.929 5.1876 -- 198 1740 0.1454 0.2038 -- 100.0
X Ray Diffraction 5.1876 5.5107 -- 183 1761 0.1425 0.2132 -- 100.0
X Ray Diffraction 5.5107 5.9331 -- 197 1722 0.1399 0.1967 -- 100.0
X Ray Diffraction 5.9331 6.5245 -- 176 1776 0.1565 0.2224 -- 100.0
X Ray Diffraction 6.5245 7.4556 -- 217 1729 0.1624 0.2648 -- 100.0
X Ray Diffraction 7.4556 9.3448 -- 198 1783 0.157 0.2121 -- 100.0
X Ray Diffraction 9.3448 29.7763 -- 207 1772 0.19 0.2246 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.086
f_dihedral_angle_d 17.128
f_angle_d 1.266
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16403
Nucleic Acid Atoms 0
Heterogen Atoms 225
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS/PHENIX Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
CNS version: 1.2/PHENIX (phenix.refine: 1.8_1069) refinement
CNS/PHENIX model building
HKL-2000 data collection