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experimental modelOtherrigid body refinement (refmac5/dimple) of a currently unpublished, isomorphous structure of a similar MBD2-DNA complex against current data.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 DROP29120% PEG-3350, 0.2 M potassium dihydrogen phosphate
Crystal Properties
Matthews coefficientSolvent content
2.856.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.912α = 84.48
b = 40.015β = 85.91
c = 105.89γ = 62.77
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-10.97934CLSI08ID-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
11.9935.4992.60.0360.0490.0330.99811.31.933843
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)
11.992.05630.5780.7860.530.5881.7

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-FreeR-Free Selection DetailsMean 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X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTrigid body refinement (refmac5/dimple) of a currently unpublished, isomorphous structure of a similar MBD2-DNA complex against current data.2.335.12191480895.390.23310.23160.2717thin resolution shells (sftools)48.293
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]
-0.53-0.830.980.87-0.78-1.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.992
r_dihedral_angle_4_deg18.842
r_dihedral_angle_3_deg14.053
r_dihedral_angle_1_deg6.669
r_mcangle_it2.17
r_angle_refined_deg1.793
r_mcbond_it1.353
r_mcbond_other1.352
r_angle_other_deg1.219
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.992
r_dihedral_angle_4_deg18.842
r_dihedral_angle_3_deg14.053
r_dihedral_angle_1_deg6.669
r_mcangle_it2.17
r_angle_refined_deg1.793
r_mcbond_it1.353
r_mcbond_other1.352
r_angle_other_deg1.219
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2035
Nucleic Acid Atoms974
Solvent Atoms25
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing