X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details 20% PEG 3350, 0.1M sodium acetate trihydrate, 6mM CHAPSO, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.72 α = 90
b = 68.13 β = 90
c = 76.31 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 MARMOSAIC 300 mm CCD -- 2013-07-30
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.97936 APS 23-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
1.35 50 97.9 0.078 0.078 -- 5.5 379104 n/a 0.0 -3.0 --
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)
1.35 1.4 85.5 0.513 0.513 2.814 3.9 379104

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 1.351 38.153 -- 1.33 68398 68398 3413 97.68 -- 0.1727 0.1713 0.1984 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 1.3508 1.3701 -- 108 2118 0.2512 0.2228 -- 78.0
X Ray Diffraction 1.3701 1.3906 -- 116 2396 0.2327 0.2732 -- 87.0
X Ray Diffraction 1.3906 1.4123 -- 137 2546 0.2183 0.2435 -- 93.0
X Ray Diffraction 1.4123 1.4354 -- 142 2670 0.2087 0.2295 -- 98.0
X Ray Diffraction 1.4354 1.4602 -- 143 2723 0.1895 0.1899 -- 99.0
X Ray Diffraction 1.4602 1.4867 -- 145 2737 0.1803 0.202 -- 100.0
X Ray Diffraction 1.4867 1.5153 -- 144 2726 0.179 0.1818 -- 100.0
X Ray Diffraction 1.5153 1.5463 -- 145 2784 0.1703 0.2244 -- 100.0
X Ray Diffraction 1.5463 1.5799 -- 143 2715 0.1622 0.2013 -- 100.0
X Ray Diffraction 1.5799 1.6167 -- 144 2728 0.1612 0.1722 -- 100.0
X Ray Diffraction 1.6167 1.6571 -- 145 2762 0.1606 0.1849 -- 100.0
X Ray Diffraction 1.6571 1.7019 -- 145 2752 0.1596 0.1769 -- 100.0
X Ray Diffraction 1.7019 1.752 -- 145 2753 0.172 0.1949 -- 100.0
X Ray Diffraction 1.752 1.8085 -- 144 2749 0.1684 0.2195 -- 100.0
X Ray Diffraction 1.8085 1.8731 -- 146 2755 0.1669 0.1866 -- 100.0
X Ray Diffraction 1.8731 1.9481 -- 145 2762 0.1689 0.1791 -- 99.0
X Ray Diffraction 1.9481 2.0368 -- 145 2759 0.1686 0.1884 -- 100.0
X Ray Diffraction 2.0368 2.1442 -- 146 2781 0.1656 0.1726 -- 100.0
X Ray Diffraction 2.1442 2.2785 -- 140 2687 0.1679 0.2009 -- 96.0
X Ray Diffraction 2.2785 2.4544 -- 146 2779 0.1695 0.2058 -- 100.0
X Ray Diffraction 2.4544 2.7013 -- 149 2819 0.1794 0.2213 -- 100.0
X Ray Diffraction 2.7013 3.0921 -- 147 2807 0.1763 0.1943 -- 100.0
X Ray Diffraction 3.0921 3.8951 -- 147 2757 0.1679 0.2059 -- 97.0
X Ray Diffraction 3.8951 38.1687 -- 156 2920 0.158 0.1894 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.115
f_chiral_restr 0.048
f_dihedral_angle_d 13.466
f_bond_d 0.006
f_plane_restr 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2091
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 234

Software

Software
Software Name Purpose
HKL-2000 data collection
EPMR phasing
PHENIX refinement version: (phenix.refine: 1.9_1692)
HKL-2000 data reduction
HKL-2000 data scaling