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GAS41 YEATS domain in complex with DLG-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 1260 mM Ammonium sulfate, 100 mM HEPES, pH 7.5, 25% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.53 51.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.499 α = 90 b = 62.619 β = 93.342 c = 84.029 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 CCD MARMOSAIC 300 mm CCD 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 50 99.6 0.098 24.98 3.6 31700
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 0.598 2.04 3.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 41.978 31687 1487 99.332 0.199 0.1965 0.2002 0.2576 0.2585 56.701
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] 4.568 -2.627 -4.961 0.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.191 r_dihedral_angle_3_deg 13.522 r_lrange_other 12.481 r_lrange_it 12.48 r_dihedral_angle_2_deg 11.508 r_scangle_it 9.171 r_scangle_other 9.17 r_mcangle_other 8.173 r_mcangle_it 8.172 r_dihedral_angle_1_deg 7.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.191 r_dihedral_angle_3_deg 13.522 r_lrange_other 12.481 r_lrange_it 12.48 r_dihedral_angle_2_deg 11.508 r_scangle_it 9.171 r_scangle_other 9.17 r_mcangle_other 8.173 r_mcangle_it 8.172 r_dihedral_angle_1_deg 7.585 r_scbond_it 6.245 r_scbond_other 6.244 r_mcbond_it 5.726 r_mcbond_other 5.698 r_dihedral_angle_other_2_deg 5.637 r_angle_refined_deg 1.881 r_angle_other_deg 0.553 r_symmetry_nbd_other 0.196 r_nbd_refined 0.193 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.179 r_nbd_other 0.146 r_symmetry_nbd_refined 0.136 r_symmetry_nbtor_other 0.091 r_symmetry_xyhbond_nbd_refined 0.078 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3962 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing