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Structure of GDP-bound GM4951
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other GTP-bound GM4951
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 36% tacsimate pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.11 60.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.323 α = 87.49 b = 100.64 β = 78.52 c = 152.355 γ = 89.91
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 2022-07-20 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 2.508 49.72 91.1 0.754 8.7 2.5 108885
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 2.508 2.54 0.494
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.51 49.72 103554 5324 90.56 0.23195 0.22978 0.2735 0.2683 RANDOM 74.994
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] -0.25 0.06 0.11 0.39 0.26 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.265 r_long_range_B_refined 17.529 r_long_range_B_other 17.529 r_scangle_other 11.8 r_dihedral_angle_2_deg 10.654 r_mcangle_it 10.449 r_mcangle_other 10.449 r_scbond_it 7.737 r_scbond_other 7.735 r_mcbond_it 6.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.265 r_long_range_B_refined 17.529 r_long_range_B_other 17.529 r_scangle_other 11.8 r_dihedral_angle_2_deg 10.654 r_mcangle_it 10.449 r_mcangle_other 10.449 r_scbond_it 7.737 r_scbond_other 7.735 r_mcbond_it 6.978 r_mcbond_other 6.978 r_dihedral_angle_1_deg 6.514 r_angle_refined_deg 1.381 r_angle_other_deg 0.482 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 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 19075 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 210
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing