X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
othercurrently unpublished model of MBD2-DNA complex

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529127% PEG-3350, 0.1 M Bis-Tris, 0.15 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.6253

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.473α = 90
b = 36.933β = 108.25
c = 104.076γ = 90
Symmetry
Space GroupC 1 2 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
11.8449.42990.0520.0630.0340.9979.83.222367
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)
11.841.8891.31.2441.5010.8280.343

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X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTcurrently unpublished model of MBD2-DNA complex1.844921271109598.960.21530.21370.246849.509
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]
-0.13-0.060.010.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.368
r_dihedral_angle_4_deg20.662
r_dihedral_angle_3_deg11.697
r_dihedral_angle_1_deg6.071
r_mcangle_it2.027
r_angle_refined_deg1.758
r_mcbond_other1.376
r_mcbond_it1.375
r_angle_other_deg1.182
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.368
r_dihedral_angle_4_deg20.662
r_dihedral_angle_3_deg11.697
r_dihedral_angle_1_deg6.071
r_mcangle_it2.027
r_angle_refined_deg1.758
r_mcbond_other1.376
r_mcbond_it1.375
r_angle_other_deg1.182
r_chiral_restr0.099
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 Atoms996
Nucleic Acid Atoms487
Solvent Atoms41
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing