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Structure of GDP-bound GM4951_N86K mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other GDP-bound GM4951
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M Tris pH 8.5 and 15% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.552 α = 106.58 b = 67.36 β = 100.73 c = 70.927 γ = 106.78
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 2023-04-05 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 3.3 47.91 89.9 0.966 13.77 2.5 11878
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 3.3 3.36 0.89
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 3.31 47.91 9449 467 74.67 0.27721 0.27484 0.2772 0.32684 0.3336 RANDOM 38.319
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] -0.09 0.02 0.16 0.16 -0.12 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.734 r_long_range_B_refined 9.877 r_long_range_B_other 9.877 r_dihedral_angle_1_deg 4.547 r_dihedral_angle_2_deg 4.506 r_mcangle_it 3.808 r_mcangle_other 3.807 r_scangle_other 3.789 r_scbond_it 2.211 r_scbond_other 2.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.734 r_long_range_B_refined 9.877 r_long_range_B_other 9.877 r_dihedral_angle_1_deg 4.547 r_dihedral_angle_2_deg 4.506 r_mcangle_it 3.808 r_mcangle_other 3.807 r_scangle_other 3.789 r_scbond_it 2.211 r_scbond_other 2.211 r_mcbond_it 2.192 r_mcbond_other 2.192 r_angle_refined_deg 1.509 r_angle_other_deg 0.73 r_chiral_restr 0.072 r_bond_refined_d 0.028 r_bond_other_d 0.016 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 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 6101 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing