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

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_bond_d 0.001
f_angle_d 0.366
f_plane_restr 0.001
f_dihedral_angle_d 15.422
f_chiral_restr 0.02
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

Software
Software Name Purpose
PHENIX refinement version: 1.8.2_1309
PDB_EXTRACT data extraction version: 3.11
ADSC data collection version: Quantum
XDS data reduction
XDS data scaling
SHEX-D phasing
PHENIX phasing