X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 20%(v/v) 2-Propanol, 0.1M MES monohydrate, 20%(w/v) Polyethylene glycol monomethyl ester 2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.28 α = 90
b = 46.28 β = 90
c = 314.38 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-04-30
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(III) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSRRC BEAMLINE BL13B1 0.9999 NSRRC BL13B1

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 30 98.9 -- 0.06 -- 3.0 58869 58869 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)
1.9 1.97 99.9 -- 0.353 3.98 3.1 5942

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 1.9 23.27 -- 1.97 58768 58768 4567 98.9 -- 0.1877 0.1847 0.2228 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 1.8997 1.9213 -- 142 1923 0.2564 0.3614 -- 100.0
X Ray Diffraction 1.9213 1.9439 -- 157 1806 0.2298 0.2873 -- 100.0
X Ray Diffraction 1.9439 1.9676 -- 150 1758 0.2221 0.2854 -- 100.0
X Ray Diffraction 1.9676 1.9925 -- 160 1873 0.2189 0.256 -- 100.0
X Ray Diffraction 1.9925 2.0187 -- 146 1842 0.2168 0.2888 -- 100.0
X Ray Diffraction 2.0187 2.0463 -- 170 1780 0.2082 0.2623 -- 100.0
X Ray Diffraction 2.0463 2.0755 -- 154 1824 0.1946 0.2456 -- 100.0
X Ray Diffraction 2.0755 2.1065 -- 166 1890 0.2044 0.2575 -- 100.0
X Ray Diffraction 2.1065 2.1394 -- 160 1731 0.1875 0.2591 -- 100.0
X Ray Diffraction 2.1394 2.1745 -- 148 1824 0.2067 0.2855 -- 100.0
X Ray Diffraction 2.1745 2.2119 -- 169 1846 0.2052 0.2593 -- 100.0
X Ray Diffraction 2.2119 2.2521 -- 156 1764 0.1898 0.2767 -- 100.0
X Ray Diffraction 2.2521 2.2954 -- 146 1896 0.1967 0.2681 -- 100.0
X Ray Diffraction 2.2954 2.3422 -- 142 1802 0.1975 0.2826 -- 100.0
X Ray Diffraction 2.3422 2.3931 -- 174 1782 0.1879 0.2454 -- 100.0
X Ray Diffraction 2.3931 2.4487 -- 143 1908 0.1955 0.2229 -- 100.0
X Ray Diffraction 2.4487 2.5099 -- 146 1761 0.1876 0.2499 -- 100.0
X Ray Diffraction 2.5099 2.5776 -- 151 1892 0.1955 0.2866 -- 100.0
X Ray Diffraction 2.5776 2.6534 -- 145 1792 0.2022 0.2449 -- 100.0
X Ray Diffraction 2.6534 2.7389 -- 171 1811 0.1951 0.2509 -- 100.0
X Ray Diffraction 2.7389 2.8366 -- 174 1768 0.1845 0.2289 -- 99.0
X Ray Diffraction 2.8366 2.95 -- 142 1818 0.1859 0.21 -- 99.0
X Ray Diffraction 2.95 3.084 -- 162 1863 0.1866 0.2437 -- 99.0
X Ray Diffraction 3.084 3.2461 -- 140 1733 0.1803 0.2033 -- 98.0
X Ray Diffraction 3.2461 3.4489 -- 161 1710 0.1722 0.1955 -- 96.0
X Ray Diffraction 3.4489 3.7142 -- 144 1761 0.16 0.1928 -- 95.0
X Ray Diffraction 3.7142 4.0862 -- 138 1694 0.1538 0.1699 -- 93.0
X Ray Diffraction 4.0862 4.6733 -- 134 1772 0.1491 0.1755 -- 95.0
X Ray Diffraction 4.6733 5.8722 -- 134 1811 0.1777 0.171 -- 99.0
X Ray Diffraction 5.8722 23.2715 -- 142 1766 0.1945 0.1849 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.8563
Anisotropic B[1][1] 2.5911
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.5911
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.1821
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.563
f_plane_restr 0.004
f_chiral_restr 0.065
f_angle_d 0.93
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6387
Nucleic Acid Atoms 272
Heterogen Atoms 8
Solvent Atoms 524

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
AMoRE Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
AMoRE model building
HKL-2000 data collection