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 (MAR225) MARRESEARCH -- --
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_plane_restr 0.007
f_bond_d 0.009
f_chiral_restr 0.073
f_dihedral_angle_d 21.72
f_angle_d 1.313
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
MOLREP model building
PHENIX version: (PHENIX.REFINE) refinement