6OGJ

MeCP2 MBD in complex with DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6C1Ypdb entry 6c1y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29130% PEG 2000 MME, 0.2M potassium bromide
Crystal Properties
Matthews coefficientSolvent content
1.8433.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.723α = 90
b = 90.181β = 92.57
c = 40.524γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-05-12MSINGLE 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
11.845.0998.60.0470.0560.030.999123.319585
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)
11.81.8394.11.1111.3360.7320.40631129

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 REPLACEMENTTHROUGHOUTpdb entry 6c1y1.845.0918390110998.50.22780.22610.256237.548
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]
-2.790.164.04-1.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.181
r_dihedral_angle_4_deg19.315
r_dihedral_angle_3_deg13.383
r_dihedral_angle_1_deg5.802
r_mcangle_it1.799
r_angle_refined_deg1.5
r_angle_other_deg1.327
r_mcbond_it1.092
r_mcbond_other1.091
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.181
r_dihedral_angle_4_deg19.315
r_dihedral_angle_3_deg13.383
r_dihedral_angle_1_deg5.802
r_mcangle_it1.799
r_angle_refined_deg1.5
r_angle_other_deg1.327
r_mcbond_it1.092
r_mcbond_other1.091
r_chiral_restr0.072
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1169
Nucleic Acid Atoms485
Solvent Atoms41
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing