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Crystal structure of MADS-box/MEF2D N-terminal domain complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MU6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 200 mM sodium acetate trihydrate, 100 mM Bis-Tris propane pH 6.5 and 20% w/v polyethylene glycol 3350 (PEG 3350)
Crystal Properties Matthews coefficient Solvent content 1.84 33.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.033 α = 90 b = 56.364 β = 90 c = 75.596 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 EIGER2 X 16M 2020-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9724 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 45.19 99.8 0.07 0.999 15.1 8.1 18562
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.893 0.791
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 45.19 18412 952 99.8 0.20619 0.20377 0.2047 0.25118 0.2509 RANDOM 38.396
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] 2.06 -0.43 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.65 r_dihedral_angle_4_deg 18.641 r_dihedral_angle_3_deg 16.926 r_long_range_B_refined 9.636 r_dihedral_angle_1_deg 5.812 r_scbond_it 4.936 r_mcangle_it 4.055 r_mcbond_it 2.968 r_angle_refined_deg 1.882 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.65 r_dihedral_angle_4_deg 18.641 r_dihedral_angle_3_deg 16.926 r_long_range_B_refined 9.636 r_dihedral_angle_1_deg 5.812 r_scbond_it 4.936 r_mcangle_it 4.055 r_mcbond_it 2.968 r_angle_refined_deg 1.882 r_gen_planes_refined 0.01 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1527 Nucleic Acid Atoms 574 Solvent Atoms 73 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement xia2 data reduction Aimless data scaling MOLREP phasing