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Crystal structure of compound 3-bound human Dynamin-1-like protein GTPase-BSE fusion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H1V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.05 M potassium chloride, 0.01 M magnesium chloride, 15% w/v PEG6000
Crystal Properties Matthews coefficient Solvent content 2.16 43.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.58 α = 90 b = 81.27 β = 101.19 c = 97.08 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2022-01-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97843 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.41 47.66 99.8 0.175 0.189 0.072 0.994 10.2 6.8 28133
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.5 99.9 0.966 1.043 0.391 0.735 7
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 PDB entry 4H1V 2.41 47.66 26672 1438 99.8 0.20819 0.20563 0.2112 0.25555 0.2566 RANDOM 43.259
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] -0.98 0.45 -0.73 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.636 r_dihedral_angle_4_deg 17.528 r_dihedral_angle_3_deg 14.837 r_long_range_B_refined 7.67 r_long_range_B_other 7.658 r_dihedral_angle_1_deg 6.601 r_scangle_other 5.11 r_mcangle_it 4.978 r_mcangle_other 4.977 r_scbond_it 3.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.636 r_dihedral_angle_4_deg 17.528 r_dihedral_angle_3_deg 14.837 r_long_range_B_refined 7.67 r_long_range_B_other 7.658 r_dihedral_angle_1_deg 6.601 r_scangle_other 5.11 r_mcangle_it 4.978 r_mcangle_other 4.977 r_scbond_it 3.148 r_scbond_other 3.148 r_mcbond_it 3.09 r_mcbond_other 3.09 r_angle_refined_deg 1.386 r_angle_other_deg 1.168 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5255 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing