X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 293.0
Details Bis-Tris propan, NaNO3, PEG3350, pH 8.0, vapor diffusion, sitting drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.83 α = 90
b = 217.87 β = 113.68
c = 87.24 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 RAYONIX MX225HE -- 2011-05-17
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPRING-8 BL41XU

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
2.39 44.01 97.1 0.036 -- -- -- -- 97820 -- -3.0 52.468
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)
2.39 2.54 89.8 0.259 -- 5.19 -- --

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 2.392 42.259 -- -- -- 97819 3528 97.35 -- 0.1773 0.1762 0.2082 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 2.392 2.4248 -- 116 2715 0.2275 0.237 -- 70.0
X Ray Diffraction 2.4248 2.4594 -- 120 3508 0.2167 0.2657 -- 93.0
X Ray Diffraction 2.4594 2.4962 -- 168 3844 0.2171 0.2639 -- 98.0
X Ray Diffraction 2.4962 2.5352 -- 127 3799 0.2166 0.2779 -- 100.0
X Ray Diffraction 2.5352 2.5767 -- 149 3879 0.2273 0.2713 -- 100.0
X Ray Diffraction 2.5767 2.6211 -- 148 3843 0.2211 0.2841 -- 100.0
X Ray Diffraction 2.6211 2.6688 -- 163 3832 0.2028 0.269 -- 100.0
X Ray Diffraction 2.6688 2.7201 -- 151 3843 0.2132 0.2734 -- 100.0
X Ray Diffraction 2.7201 2.7756 -- 145 3877 0.2042 0.2523 -- 100.0
X Ray Diffraction 2.7756 2.836 -- 125 3824 0.1995 0.2691 -- 100.0
X Ray Diffraction 2.836 2.9019 -- 131 3901 0.2034 0.2296 -- 100.0
X Ray Diffraction 2.9019 2.9745 -- 156 3846 0.2062 0.253 -- 99.0
X Ray Diffraction 2.9745 3.0549 -- 146 3799 0.208 0.2517 -- 99.0
X Ray Diffraction 3.0549 3.1447 -- 151 3853 0.2153 0.2835 -- 100.0
X Ray Diffraction 3.1447 3.2462 -- 154 3879 0.2014 0.2166 -- 99.0
X Ray Diffraction 3.2462 3.3622 -- 134 3825 0.1949 0.2498 -- 99.0
X Ray Diffraction 3.3622 3.4967 -- 131 3864 0.1781 0.1761 -- 99.0
X Ray Diffraction 3.4967 3.6558 -- 136 3865 0.1742 0.214 -- 99.0
X Ray Diffraction 3.6558 3.8484 -- 132 3846 0.1666 0.1703 -- 99.0
X Ray Diffraction 3.8484 4.0894 -- 143 3862 0.159 0.1915 -- 99.0
X Ray Diffraction 4.0894 4.4048 -- 156 3870 0.1481 0.1933 -- 99.0
X Ray Diffraction 4.4048 4.8475 -- 157 3837 0.1353 0.1628 -- 100.0
X Ray Diffraction 4.8475 5.5476 -- 142 3872 0.1499 0.1693 -- 100.0
X Ray Diffraction 5.5476 6.9843 -- 130 3898 0.1708 0.1887 -- 100.0
X Ray Diffraction 6.9843 42.2658 -- 117 3301 0.1593 0.1738 -- 84.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.2137
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.735
f_plane_restr 0.006
f_chiral_restr 0.053
f_angle_d 1.261
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 17474
Nucleic Acid Atoms 0
Heterogen Atoms 520
Solvent Atoms 365

Software

Computing
Computing Package Purpose
BSS Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction