X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherrigid body refinement (refmac5/dimple) of a currently unpublished, isomorphous structure of a similar MBD2-DNA complex against current data.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529125% PEG-3350, 0.1 M Bis-Tris
Crystal Properties
Matthews coefficientSolvent content
2.957.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.013α = 84.5
b = 40.198β = 85.48
c = 105.158γ = 62.71
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1235.6494.80.040.0540.0370.998101.934483
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0581.40.761.0320.6940.4651.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTrigid body refinement (refmac5/dimple) of a currently unpublished, isomorphous structure of a similar MBD2-DNA complex against current data.2.334.82207982196.090.2340.23270.267749.143
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-1.7-0.480.310.580.040.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.659
r_dihedral_angle_4_deg20.108
r_dihedral_angle_3_deg14.439
r_dihedral_angle_1_deg6.78
r_mcangle_it2.161
r_angle_refined_deg1.786
r_mcbond_it1.365
r_mcbond_other1.357
r_angle_other_deg1.23
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.659
r_dihedral_angle_4_deg20.108
r_dihedral_angle_3_deg14.439
r_dihedral_angle_1_deg6.78
r_mcangle_it2.161
r_angle_refined_deg1.786
r_mcbond_it1.365
r_mcbond_other1.357
r_angle_other_deg1.23
r_chiral_restr0.095
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2024
Nucleic Acid Atoms972
Solvent Atoms29
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing