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GID4 in complex with Compound 18
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CD9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Na HEPES pH 7.0,0.1 M lithium sulfate, 22.5% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.255 α = 90 b = 41.752 β = 90 c = 103.205 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 2022-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03321 PETRA III, DESY P11
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 1.79 41.75 97.1 0.988 5.68 4.38 30931
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 1.79 1.9 0.303
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 38.73 13268 699 97.51 0.27873 0.2757 0.2852 0.33584 0.3457 RANDOM 31.348
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] -3.06 5.44 -2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.299 r_dihedral_angle_3_deg 17.744 r_dihedral_angle_4_deg 12.196 r_dihedral_angle_1_deg 8.535 r_long_range_B_refined 7.766 r_long_range_B_other 7.766 r_scangle_other 4.448 r_mcangle_other 4.109 r_mcangle_it 4.108 r_scbond_it 2.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.299 r_dihedral_angle_3_deg 17.744 r_dihedral_angle_4_deg 12.196 r_dihedral_angle_1_deg 8.535 r_long_range_B_refined 7.766 r_long_range_B_other 7.766 r_scangle_other 4.448 r_mcangle_other 4.109 r_mcangle_it 4.108 r_scbond_it 2.731 r_scbond_other 2.729 r_mcbond_it 2.636 r_mcbond_other 2.626 r_angle_refined_deg 1.533 r_angle_other_deg 1.19 r_chiral_restr 0.061 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1335 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing