6MIK

Crystal structure of host-guest complex with PP hachimoji DNA


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 8 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.15 α = 90
b = 145.85 β = 90
c = 46.85 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2018-05-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL14-1 1.19499 SSRL BL14-1

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
1.7 39.42 99.5 0.095 -- -- 4.5 -- 42311 -- -- 24.62
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)
1.7 1.73 99.3 0.836 -- -- 4.4 --

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 1.7 39.416 -- 1.34 -- 42253 2013 99.44 -- 0.215 0.2134 0.2468 --
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 1.7003 1.7428 -- 143 2799 0.2875 0.2733 0.0 99.0
X Ray Diffraction 1.7428 1.7899 -- 141 2859 0.2502 0.2793 0.0 100.0
X Ray Diffraction 1.7899 1.8426 -- 124 2859 0.2413 0.3039 0.0 100.0
X Ray Diffraction 1.8426 1.902 -- 161 2815 0.241 0.2695 0.0 99.0
X Ray Diffraction 1.902 1.97 -- 128 2842 0.2313 0.2684 0.0 99.0
X Ray Diffraction 1.97 2.0489 -- 156 2828 0.2233 0.2576 0.0 99.0
X Ray Diffraction 2.0489 2.1421 -- 123 2879 0.2161 0.2762 0.0 100.0
X Ray Diffraction 2.1421 2.2551 -- 130 2859 0.2134 0.2681 0.0 100.0
X Ray Diffraction 2.2551 2.3963 -- 145 2879 0.2143 0.213 0.0 100.0
X Ray Diffraction 2.3963 2.5813 -- 149 2853 0.2144 0.2596 0.0 100.0
X Ray Diffraction 2.5813 2.841 -- 154 2873 0.2306 0.2544 0.0 99.0
X Ray Diffraction 2.841 3.252 -- 135 2936 0.2228 0.2661 0.0 100.0
X Ray Diffraction 3.252 4.0964 -- 173 2839 0.2028 0.2332 0.0 98.0
X Ray Diffraction 4.0964 39.4266 -- 151 3120 0.1902 0.2234 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.4984
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 10.38
f_angle_d 0.966
f_plane_restr 0.007
f_bond_d 0.007
f_chiral_restr 0.063
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1989
Nucleic Acid Atoms 332
Heterogen Atoms 0
Solvent Atoms 191

Software

Software
Software Name Purpose
PHENIX refinement version: 1.11.1_2575
Aimless data scaling
PDB_EXTRACT data extraction version: 3.24
XDS data reduction
PHASER phasing