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Human death-associated DRP-1 kinase in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A2A PDB ENTRY 2A2A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.2 M LI SULFATE, 0.1 M TRIS PH 8.5, 25 % PEG 4000, 15 % GLYCEROL, 10 MM DTT.
Crystal Properties Matthews coefficient Solvent content 2.32 46.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.21 α = 92.09 b = 60.48 β = 103.39 c = 99.28 γ = 94.16
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 20 97.5 0.06 10.7 2.2 30010 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 97.1 0.33 2.8 2.2
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 2A2A 2.8 20 28431 1497 97.8 0.206 0.203 0.2045 0.261 0.2616 RANDOM 36.52
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] 1.67 0.1 0.72 -1.03 1.74 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.914 r_dihedral_angle_4_deg 15.684 r_dihedral_angle_3_deg 14.269 r_dihedral_angle_1_deg 5.103 r_angle_refined_deg 0.882 r_scangle_it 0.86 r_mcangle_it 0.741 r_angle_other_deg 0.738 r_scbond_it 0.559 r_mcbond_it 0.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.914 r_dihedral_angle_4_deg 15.684 r_dihedral_angle_3_deg 14.269 r_dihedral_angle_1_deg 5.103 r_angle_refined_deg 0.882 r_scangle_it 0.86 r_mcangle_it 0.741 r_angle_other_deg 0.738 r_scbond_it 0.559 r_mcbond_it 0.425 r_symmetry_vdw_other 0.2 r_nbd_refined 0.189 r_nbtor_refined 0.172 r_nbd_other 0.168 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.117 r_nbtor_other 0.079 r_symmetry_hbond_refined 0.062 r_chiral_restr 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9776 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing