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GID4 in complex with Compound 1
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, HANGING DROP 293 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 1.94 36.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.107 α = 90 b = 40.568 β = 107.94 c = 51.585 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 PIXEL DECTRIS PILATUS 2M-F 2020-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.03318 SLS X06DA
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 2.26 49.08 99.64 0.1081 5.26 2 7111
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 2.26 2.35 0.6377
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 2.26 49.08 6758 354 99.71 0.21591 0.21163 0.2183 0.29566 0.2879 RANDOM 34.422
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] 1.29 0.68 -1.66 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.128 r_dihedral_angle_3_deg 16.128 r_dihedral_angle_1_deg 7.787 r_long_range_B_refined 7.039 r_long_range_B_other 7.037 r_mcangle_it 4.342 r_mcangle_other 4.341 r_scangle_other 4.332 r_mcbond_it 2.625 r_mcbond_other 2.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.128 r_dihedral_angle_3_deg 16.128 r_dihedral_angle_1_deg 7.787 r_long_range_B_refined 7.039 r_long_range_B_other 7.037 r_mcangle_it 4.342 r_mcangle_other 4.341 r_scangle_other 4.332 r_mcbond_it 2.625 r_mcbond_other 2.622 r_scbond_it 2.609 r_scbond_other 2.607 r_angle_refined_deg 1.22 r_angle_other_deg 0.436 r_chiral_restr 0.057 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1348 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing