5NRS

Human DNMT3B PWWP domain in complex with N,N-bis(2-hydroxypropyl)ethanolamine


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 298.0
Details 0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.93 α = 90
b = 74.93 β = 90
c = 157.47 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2015-12-06
Diffraction Radiation
Monochromator Protocol
channel cut monochromator crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978570 SOLEIL PROXIMA 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
2.3 40.81 99.5 0.05 -- -- 9.3 -- 23390 -- -- 61.9
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)
2.3 2.44 96.9 0.893 -- 1.89 7.2 3609

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 2.3 40.81 -- 1.37 -- 23383 1170 99.46 -- 0.1977 0.1951 0.2477 --
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 2.2989 2.4035 -- 139 2634 0.3513 0.3919 0.0 96.0
X Ray Diffraction 2.4035 2.5302 -- 144 2734 0.2962 0.3437 0.0 100.0
X Ray Diffraction 2.5302 2.6887 -- 145 2752 0.2471 0.3167 0.0 100.0
X Ray Diffraction 2.6887 2.8963 -- 145 2758 0.2282 0.2647 0.0 100.0
X Ray Diffraction 2.8963 3.1876 -- 145 2756 0.2317 0.2734 0.0 100.0
X Ray Diffraction 3.1876 3.6486 -- 147 2792 0.1986 0.2535 0.0 100.0
X Ray Diffraction 3.6486 4.5959 -- 149 2825 0.1711 0.2355 0.0 100.0
X Ray Diffraction 4.5959 40.8166 -- 156 2962 0.1674 0.2123 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 60.46
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.036
f_angle_d 1.164
f_plane_restr 0.005
f_chiral_restr 0.078
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2128
Nucleic Acid Atoms 0
Heterogen Atoms 49
Solvent Atoms 60

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.22
PHASER phasing
XDS data reduction

We're sorry, but a portion of the page could not be displayed.
If time permits, please submit a detailed description of the issue on our Contact Us page.