X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 50 mM Bis-Tris (HCl) pH 6.5, 300 mM Li2SO4, and 20% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.38 α = 90
b = 108.47 β = 90
c = 266.89 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- --
CCD ADSC QUANTUM 315r -- --
CCD ADSC QUANTUM 315 -- --
CCD ADSC QUANTUM 315 -- 2012-08-02
Diffraction Radiation
Monochromator Protocol
Kohzu HLD8-24 monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 0.9793 ALS 5.0.2
SYNCHROTRON ALS BEAMLINE 5.0.1 0.9793 ALS 5.0.1
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9793 APS 24-ID-C
SYNCHROTRON APS BEAMLINE 24-ID-E 0.9793 APS 24-ID-E

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
3.2 28.42 98.9 0.062 -- -- 6.1 -- n/a 1.5 1.5 128.66
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)
3.2 3.2653 98.0 -- -- -- -- --

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, SAD 3.2 28.416 -- 1.34 46354 45770 2318 98.74 -- 0.1984 0.1957 0.2514 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 3.2 3.2653 -- 127 2486 0.3472 0.38 -- 98.0
X Ray Diffraction 3.2653 3.3362 -- 143 2622 0.3214 0.3475 -- 99.0
X Ray Diffraction 3.3362 3.4136 -- 126 2537 0.3176 0.377 -- 100.0
X Ray Diffraction 3.4136 3.4989 -- 135 2613 0.3075 0.3229 -- 99.0
X Ray Diffraction 3.4989 3.5933 -- 125 2561 0.2867 0.3292 -- 100.0
X Ray Diffraction 3.5933 3.6988 -- 135 2626 0.2676 0.3333 -- 99.0
X Ray Diffraction 3.6988 3.8179 -- 123 2537 0.2458 0.2903 -- 100.0
X Ray Diffraction 3.8179 3.954 -- 123 2606 0.241 0.299 -- 100.0
X Ray Diffraction 3.954 4.1119 -- 137 2619 0.2135 0.3009 -- 100.0
X Ray Diffraction 4.1119 4.2984 -- 162 2535 0.2036 0.2286 -- 100.0
X Ray Diffraction 4.2984 4.5242 -- 161 2559 0.1933 0.2729 -- 100.0
X Ray Diffraction 4.5242 4.8064 -- 168 2523 0.1899 0.2246 -- 100.0
X Ray Diffraction 4.8064 5.1754 -- 132 2609 0.1849 0.2452 -- 100.0
X Ray Diffraction 5.1754 5.6925 -- 175 2555 0.1563 0.2487 -- 99.0
X Ray Diffraction 5.6925 6.5076 -- 132 2517 0.1721 0.256 -- 98.0
X Ray Diffraction 6.5076 8.1665 -- 125 2533 0.1757 0.2442 -- 97.0
X Ray Diffraction 8.1665 28.4168 -- 89 2414 0.1613 0.181 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 128.001
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.422
f_plane_restr 0.001
f_chiral_restr 0.02
f_angle_d 0.366
f_bond_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1048
Nucleic Acid Atoms 7586
Heterogen Atoms 86
Solvent Atoms 22

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
xds Data Reduction (intensity integration)
xds Data Reduction (data scaling)
SHEX-D, PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement