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GID4 in complex with Compound 21
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 7.5,0.1 M lithium sulfate, 22.5% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.23 44.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.273 α = 90 b = 41.93 β = 90 c = 103.135 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 2022-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0333 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 41.93 99.6 0.996 6.2 7.31 16864
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 0.2
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 (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 37.54 11708 617 99.68 0.22151 0.21987 0.2269 0.25298 0.2544 RANDOM 37.221
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] -1.04 1.76 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.845 r_dihedral_angle_3_deg 15.558 r_long_range_B_refined 7.812 r_long_range_B_other 7.81 r_dihedral_angle_1_deg 7.632 r_scangle_other 5.848 r_mcangle_other 4.736 r_mcangle_it 4.732 r_scbond_it 3.732 r_scbond_other 3.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.845 r_dihedral_angle_3_deg 15.558 r_long_range_B_refined 7.812 r_long_range_B_other 7.81 r_dihedral_angle_1_deg 7.632 r_scangle_other 5.848 r_mcangle_other 4.736 r_mcangle_it 4.732 r_scbond_it 3.732 r_scbond_other 3.731 r_mcbond_it 3.131 r_mcbond_other 3.124 r_angle_refined_deg 1.581 r_angle_other_deg 0.515 r_chiral_restr 0.074 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 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 1331 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing