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Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 0.09 M Na Acetate pH 4.5, 2.7 % PEG Smears Medium, 6.3 % MPD, 0.5 n-octyl-beta-D-Glucoside and 3% D-Trehalose
Crystal Properties Matthews coefficient Solvent content 3.28 62.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.604 α = 90 b = 102.533 β = 90 c = 154.002 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 EIGER X 16M 2022-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 85.35 100 1 22.4 13.7 126840
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 100 0.796 1.9 14.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 59.253 126748 6216 99.956 0.162 0.1604 0.1723 0.1881 0.196 RANDOM 32.934
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] -0.018 0.009 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.032 r_dihedral_angle_3_deg 13.735 r_dihedral_angle_2_deg 11.067 r_lrange_it 7.397 r_lrange_other 7.241 r_dihedral_angle_1_deg 6.575 r_scangle_it 5.546 r_scangle_other 5.546 r_scbond_it 3.832 r_scbond_other 3.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.032 r_dihedral_angle_3_deg 13.735 r_dihedral_angle_2_deg 11.067 r_lrange_it 7.397 r_lrange_other 7.241 r_dihedral_angle_1_deg 6.575 r_scangle_it 5.546 r_scangle_other 5.546 r_scbond_it 3.832 r_scbond_other 3.832 r_mcangle_it 3.116 r_mcangle_other 3.116 r_mcbond_it 2.302 r_mcbond_other 2.302 r_angle_refined_deg 1.598 r_dihedral_angle_other_2_deg 0.584 r_angle_other_deg 0.554 r_nbd_refined 0.284 r_symmetry_nbd_refined 0.211 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.166 r_nbd_other 0.14 r_chiral_restr_other 0.123 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5697 Nucleic Acid Atoms Solvent Atoms 802 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing