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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 6.5 291 50% precipitant mix 4, 0.1M buffer system 1, 0.06M divalents (morpheus A4)
Crystal Properties Matthews coefficient Solvent content 1.87 34.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.47 α = 90 b = 51.976 β = 90 c = 66.304 γ = 90
Symmetry Space Group P 21 21 21
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 2018-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
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 1.6 40.91 99.8 0.06 0.065 0.026 1 17.5 6.1 18969
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 1.6 1.63 97.3 1.835 2.092 0.982 0.366 4.1 891
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 1.65 40.9 15648 1773 99.96 0.2289 0.2259 0.2368 0.2552 0.2601 29.887
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] 0.67 -1.75 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.027 r_dihedral_angle_4_deg 24.813 r_dihedral_angle_3_deg 13.015 r_dihedral_angle_1_deg 6.407 r_angle_refined_deg 1.743 r_mcangle_it 1.649 r_angle_other_deg 1.524 r_mcbond_other 1.037 r_mcbond_it 1.036 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.027 r_dihedral_angle_4_deg 24.813 r_dihedral_angle_3_deg 13.015 r_dihedral_angle_1_deg 6.407 r_angle_refined_deg 1.743 r_mcangle_it 1.649 r_angle_other_deg 1.524 r_mcbond_other 1.037 r_mcbond_it 1.036 r_chiral_restr 0.077 r_gen_planes_refined 0.018 r_bond_refined_d 0.011 r_gen_planes_other 0.008 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 585 Nucleic Acid Atoms 487 Solvent Atoms 56 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing