X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Details RESERVOIR: 2 M (NH4)2SO4, 100 MM BIS-TRIS, PH 5.5. SAMPLE: 30 MG/ML PROTEIN IN 50 MM BIS-TRIS, PH 6.0.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.31 α = 90
b = 66.11 β = 90
c = 133.74 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 (MAR165) MARRESEARCH MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M). 2011-12-03
Diffraction Radiation
Monochromator Protocol
BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-2 -- MAX II I911-2

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
1.6 30 99.0 0.04 -- -- 8.6 -- 62765 -- 15.0 19.66
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)
1.6 1.7 23.0 0.14 -- 6.0 9.6 --

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 1.6 24.795 -- 2.0 -- 62748 3182 99.32 -- 0.1874 0.1862 0.2084 --
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 1.6 1.6239 -- 121 2411 0.2932 0.3237 -- 94.0
X Ray Diffraction 1.6239 1.6493 -- 139 2573 0.272 0.3355 -- 100.0
X Ray Diffraction 1.6493 1.6763 -- 139 2557 0.2458 0.2855 -- 99.0
X Ray Diffraction 1.6763 1.7052 -- 125 2552 0.2256 0.273 -- 100.0
X Ray Diffraction 1.7052 1.7362 -- 151 2582 0.2255 0.2462 -- 100.0
X Ray Diffraction 1.7362 1.7696 -- 127 2571 0.2106 0.2583 -- 100.0
X Ray Diffraction 1.7696 1.8057 -- 139 2562 0.1952 0.2154 -- 100.0
X Ray Diffraction 1.8057 1.8449 -- 130 2638 0.1898 0.2469 -- 100.0
X Ray Diffraction 1.8449 1.8878 -- 144 2551 0.1831 0.2057 -- 100.0
X Ray Diffraction 1.8878 1.935 -- 140 2562 0.1751 0.2143 -- 100.0
X Ray Diffraction 1.935 1.9873 -- 136 2581 0.1769 0.2134 -- 100.0
X Ray Diffraction 1.9873 2.0458 -- 154 2568 0.1794 0.2135 -- 100.0
X Ray Diffraction 2.0458 2.1118 -- 134 2601 0.173 0.1914 -- 100.0
X Ray Diffraction 2.1118 2.1872 -- 142 2600 0.1737 0.2003 -- 100.0
X Ray Diffraction 2.1872 2.2747 -- 128 2601 0.1801 0.1977 -- 100.0
X Ray Diffraction 2.2747 2.3782 -- 137 2603 0.178 0.2041 -- 100.0
X Ray Diffraction 2.3782 2.5034 -- 112 2646 0.1817 0.2081 -- 100.0
X Ray Diffraction 2.5034 2.6601 -- 126 2638 0.1884 0.1867 -- 100.0
X Ray Diffraction 2.6601 2.8652 -- 146 2603 0.1967 0.2501 -- 100.0
X Ray Diffraction 2.8652 3.1531 -- 153 2643 0.1955 0.2209 -- 100.0
X Ray Diffraction 3.1531 3.6081 -- 167 2611 0.169 0.1927 -- 100.0
X Ray Diffraction 3.6081 4.5413 -- 145 2659 0.1536 0.1651 -- 99.0
X Ray Diffraction 4.5413 24.7983 -- 147 2653 0.208 0.207 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.5168
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.1275
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.6443
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.075
f_dihedral_angle_d 11.984
f_angle_d 1.061
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2438
Nucleic Acid Atoms 0
Heterogen Atoms 70
Solvent Atoms 442

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
PHENIX model building