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Structure of Parkin E3 ligase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I1F PDB ENTRY 4I1F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 283 0.1 M Tris, pH 6.5, 0.2 M sodium chloride, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 383K
Crystal Properties Matthews coefficient Solvent content 2.65 53.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.11 α = 90 b = 133.93 β = 90 c = 66.21 γ = 90
Symmetry Space Group C 2 2 21
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 RIGAKU SATURN 944+ 2012-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 16.971 82 0.111 12.1 6.1 26566 21783
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 2.11 36.3 0.398 3.6 5.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4I1F 2 16.971 21783 1089 81.95 0.18239 0.18068 0.21537 0.191 RANDOM 20.871
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] -0.68 0.24 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.57 r_dihedral_angle_4_deg 16.963 r_dihedral_angle_3_deg 14.071 r_dihedral_angle_1_deg 6.75 r_angle_refined_deg 1.842 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.57 r_dihedral_angle_4_deg 16.963 r_dihedral_angle_3_deg 14.071 r_dihedral_angle_1_deg 6.75 r_angle_refined_deg 1.842 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 2399 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 8
Software Software Software Name Purpose StructureStudio data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing