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 MARRESEARCH MAR165 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_angle_d 1.061
f_bond_d 0.007
f_plane_restr 0.005
f_chiral_restr 0.075
f_dihedral_angle_d 11.984
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

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
XSCALE data scaling
PHENIX phasing