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Crystal structure of human GSK3B in complex with G5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I09
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 PEG3350, Sodium Chloride, Hepes
Crystal Properties Matthews coefficient Solvent content 3.95 68.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.65 α = 90 b = 85.36 β = 90 c = 178.36 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 PILATUS 2M 2021-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1 ELETTRA 5.2R
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 2.38 48.83 100 0.998 11.9 13.6 51397
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 2.38 2.48 0.46
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1I09 2.38 48.83 48674 2394 99.36 0.2439 0.2423 0.2572 0.2759 0.2859 RANDOM 63.599
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] 0.61 3.33 -3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.423 r_dihedral_angle_4_deg 15.764 r_dihedral_angle_3_deg 15.588 r_dihedral_angle_1_deg 5.95 r_angle_refined_deg 1.388 r_angle_other_deg 1.219 r_chiral_restr 0.106 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.423 r_dihedral_angle_4_deg 15.764 r_dihedral_angle_3_deg 15.588 r_dihedral_angle_1_deg 5.95 r_angle_refined_deg 1.388 r_angle_other_deg 1.219 r_chiral_restr 0.106 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5577 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing