X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details CRYSTALS WERE GROWN THROUGH REVERSE VAPOR DIFFUSION IN HANGING DROPS AT 23 C BY MIXING 1 UL IN-DNA COMPLEX SOLUTION (20 MM HEPES, PH 7.5, 500 MM NACL, 5 MM MGCL2, 2 MM TCEP AND 8% (W/V) GLYCEROL) WITH 1 UL RESERVOIR SOLUTION (50 MM NA CACODYLATE, PH 6.5, 100 MM MGCL2, 1 MM COCL3 AND 6% (V/V) ETHANOL).

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 160.62 α = 90
b = 160.62 β = 90
c = 125.09 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- --
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL - SI (220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM -- APS 22-BM

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
3.26 30 98.8 -- 0.11 -- 6.3 -- 25740 -- 2.0 75.3
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)
3.26 3.32 100.0 -- 0.62 2.0 6.3 --

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 3.263 29.141 -- 0.13 -- 24101 1223 92.66 -- 0.1868 0.1847 0.2263 --
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 3.2626 3.393 -- 131 2306 0.2935 0.3555 -- 86.0
X Ray Diffraction 3.393 3.5472 -- 115 2365 0.2427 0.2809 -- 88.0
X Ray Diffraction 3.5472 3.7339 -- 130 2447 0.2149 0.2817 -- 91.0
X Ray Diffraction 3.7339 3.9673 -- 132 2477 0.1991 0.2672 -- 91.0
X Ray Diffraction 3.9673 4.2727 -- 161 2540 0.1637 0.1865 -- 95.0
X Ray Diffraction 4.2727 4.7011 -- 132 2637 0.1383 0.1881 -- 96.0
X Ray Diffraction 4.7011 5.3776 -- 143 2644 0.1477 0.1771 -- 96.0
X Ray Diffraction 5.3776 6.7613 -- 142 2691 0.1655 0.1993 -- 96.0
X Ray Diffraction 6.7613 29.1426 -- 137 2771 0.1702 0.2089 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 9.9139
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 9.9139
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -19.8278
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.313
f_bond_d 0.009
f_dihedral_angle_d 21.72
f_plane_restr 0.007
f_chiral_restr 0.073
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4378
Nucleic Acid Atoms 1305
Heterogen Atoms 3
Solvent Atoms 3

Software

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing