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MeCP2 MBD in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C1Y pdb entry 6c1y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 30% PEG 2000 MME, 0.2M potassium bromide
Crystal Properties Matthews coefficient Solvent content 1.84 33.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.723 α = 90 b = 90.181 β = 92.57 c = 40.524 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2018-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 45.09 98.6 0.047 0.056 0.03 0.999 12 3.3 19585
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) Redundancy Number Unique Reflections (All) 1 1.8 1.83 94.1 1.111 1.336 0.732 0.406 3 1129
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 6c1y 1.8 45.09 18390 1109 98.5 0.2278 0.2261 0.2313 0.2562 0.2535 37.548
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] -2.79 0.16 4.04 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.181 r_dihedral_angle_4_deg 19.315 r_dihedral_angle_3_deg 13.383 r_dihedral_angle_1_deg 5.802 r_mcangle_it 1.799 r_angle_refined_deg 1.5 r_angle_other_deg 1.327 r_mcbond_it 1.092 r_mcbond_other 1.091 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.181 r_dihedral_angle_4_deg 19.315 r_dihedral_angle_3_deg 13.383 r_dihedral_angle_1_deg 5.802 r_mcangle_it 1.799 r_angle_refined_deg 1.5 r_angle_other_deg 1.327 r_mcbond_it 1.092 r_mcbond_other 1.091 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1169 Nucleic Acid Atoms 485 Solvent Atoms 41 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing