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Structure of GTP-bound GM4951
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1M succinic acid pH 7.0, 0.1 M HEPES pH 7.0, and 1% (wt/vol) PEG-MME 2000
Crystal Properties Matthews coefficient Solvent content 3.07 59.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.759 α = 92.31 b = 100.245 β = 101.24 c = 152.347 γ = 89.86
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 6M 2022-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
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 2.754 46.02 88.1 0.979 11.4 4.4 78604
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 2.754 2.8 0.669
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 2.75 46.02 57883 3116 68 0.21062 0.20867 0.2132 0.24659 0.2502 RANDOM 54.965
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] 0.07 0.03 -0.03 0.02 -0.05 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.866 r_long_range_B_refined 13.867 r_long_range_B_other 13.867 r_dihedral_angle_2_deg 13.468 r_scangle_other 7.203 r_mcangle_it 6.87 r_mcangle_other 6.87 r_dihedral_angle_1_deg 6 r_scbond_other 4.438 r_scbond_it 4.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.866 r_long_range_B_refined 13.867 r_long_range_B_other 13.867 r_dihedral_angle_2_deg 13.468 r_scangle_other 7.203 r_mcangle_it 6.87 r_mcangle_other 6.87 r_dihedral_angle_1_deg 6 r_scbond_other 4.438 r_scbond_it 4.437 r_mcbond_it 4.231 r_mcbond_other 4.231 r_angle_refined_deg 1.363 r_angle_other_deg 0.535 r_chiral_restr 0.065 r_bond_other_d 0.019 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 19124 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 296
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing