☰ Navigation Tabs
Transcription factor MYF5 bound to symmetrical site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 295 PME 3350, 2% MPD, 0.05M Sodium Acetate, pH 4.5
Crystal Properties Matthews coefficient Solvent content 3.09 60.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.7 α = 90 b = 33.923 β = 91.04 c = 53.729 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M 2018-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.996 83.336 91.3 0.067 0.083 0.047 6.9 2.8 5721 5721
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 92 0.912 0.912 1.119 0.638 0.8 2.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1MDY 3 53.34 5157 560 90.5 0.2332 0.2272 0.2305 0.2876 0.2903 RANDOM 99.019
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] 10.36 -8.35 -3.56 -6.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.402 r_dihedral_angle_3_deg 24.741 r_dihedral_angle_4_deg 19.762 r_dihedral_angle_1_deg 7.026 r_angle_refined_deg 1.477 r_angle_other_deg 1.471 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.402 r_dihedral_angle_3_deg 24.741 r_dihedral_angle_4_deg 19.762 r_dihedral_angle_1_deg 7.026 r_angle_refined_deg 1.477 r_angle_other_deg 1.471 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 942 Nucleic Acid Atoms 738 Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction PDB_EXTRACT data extraction XDS data scaling PHASER phasing