3C2I

The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a Methylated DNA Sequence from BDNF


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529026% PEG2000, 0.2M Ammonium acetate, 0.01M Mg acetate, 0.05M Na cacodylate pH6.5, 0.002M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.2144.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.71α = 90
b = 53.6β = 132.1
c = 65.73γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2006-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97800ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.548.79598.50.0750.0753.17.17122712284.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6490.70.3770.37725.3950

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.523.487115711533198.530.2150.2120.276RANDOM59.076
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]
0.290.070.3-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.425
r_dihedral_angle_4_deg21.077
r_dihedral_angle_3_deg20.454
r_dihedral_angle_1_deg5.524
r_angle_refined_deg1.848
r_scangle_it1.579
r_scbond_it1.001
r_mcangle_it0.898
r_mcbond_it0.693
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.425
r_dihedral_angle_4_deg21.077
r_dihedral_angle_3_deg20.454
r_dihedral_angle_1_deg5.524
r_angle_refined_deg1.848
r_scangle_it1.579
r_scbond_it1.001
r_mcangle_it0.898
r_mcbond_it0.693
r_nbtor_refined0.317
r_symmetry_vdw_refined0.231
r_nbd_refined0.219
r_xyhbond_nbd_refined0.189
r_symmetry_hbond_refined0.129
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms584
Nucleic Acid Atoms816
Solvent Atoms47
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction