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GID4 in complex with Compound 14
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 292.15 0.1 M Na HEPES 7.5, 7.5% 2-propanol, 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.97 37.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.09 α = 90 b = 40.39 β = 108.69 c = 52.87 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 EIGER X 16M 2022-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 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 1.8 36.08 98 0.99 12.75 3.84 53975
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 1.8 1.91 0.86
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 1.8 31.44 13366 704 98.12 0.18403 0.18082 0.1944 0.24357 0.2438 RANDOM 29.566
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] -1.14 -1.37 -2.28 3.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.907 r_dihedral_angle_3_deg 13.513 r_long_range_B_refined 9.552 r_long_range_B_other 9.545 r_scangle_other 8.171 r_dihedral_angle_1_deg 7.81 r_scbond_it 5.833 r_scbond_other 5.829 r_mcangle_it 5.323 r_mcangle_other 5.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.907 r_dihedral_angle_3_deg 13.513 r_long_range_B_refined 9.552 r_long_range_B_other 9.545 r_scangle_other 8.171 r_dihedral_angle_1_deg 7.81 r_scbond_it 5.833 r_scbond_other 5.829 r_mcangle_it 5.323 r_mcangle_other 5.322 r_mcbond_it 4.149 r_mcbond_other 4.135 r_angle_refined_deg 2.153 r_angle_other_deg 0.726 r_chiral_restr 0.118 r_bond_refined_d 0.016 r_gen_planes_refined 0.016 r_bond_other_d 0.001 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 1386 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing