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Crystal structure of GAS41 YEATS domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Bis-Tris buffer (pH 5.9) containing 3.3 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.93 61.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.595 α = 90 b = 52.834 β = 116.47 c = 57.864 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 CCD RAYONIX MX225HE 2016-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.575 50 99.8 0.036 29.9 3.7 27444
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.575 1.61 0.16
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 4TMP 1.58 32.96 25924 1384 99.77 0.14481 0.14411 0.1555 0.15812 0.1682 RANDOM 22.307
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] 1.66 -0.75 0.19 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.761 r_dihedral_angle_4_deg 14.812 r_dihedral_angle_3_deg 11.008 r_dihedral_angle_1_deg 6.423 r_long_range_B_refined 5.901 r_long_range_B_other 5.398 r_scangle_other 4.337 r_scbond_it 3.805 r_scbond_other 3.804 r_mcangle_it 3.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.761 r_dihedral_angle_4_deg 14.812 r_dihedral_angle_3_deg 11.008 r_dihedral_angle_1_deg 6.423 r_long_range_B_refined 5.901 r_long_range_B_other 5.398 r_scangle_other 4.337 r_scbond_it 3.805 r_scbond_other 3.804 r_mcangle_it 3.316 r_mcangle_other 3.315 r_rigid_bond_restr 2.695 r_mcbond_other 2.655 r_mcbond_it 2.645 r_angle_refined_deg 1.423 r_angle_other_deg 1.35 r_chiral_restr 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1073 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing