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Crystal Structure of Ideonella sakaiensis PET Hydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M MES pH 6.5
1.6 M MgSO4
20% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.96 58.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.868 α = 90 b = 233.852 β = 90 c = 165.076 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 110 PIXEL DECTRIS PILATUS 200K 2017-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.541870
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 2.02 116.93 95.9 0.104 9.83 6 67721
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 2.02 2.05 92.4 0.653 2 3.9
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 4cg1 2.02 116.93 61680 3205 95.73 0.17923 0.17725 0.1861 0.21664 0.2228 RANDOM 21.221
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] 2 -1.79 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.91 r_dihedral_angle_4_deg 13.062 r_dihedral_angle_3_deg 11.597 r_dihedral_angle_1_deg 6.568 r_long_range_B_refined 3.631 r_long_range_B_other 3.564 r_scangle_other 2.382 r_mcangle_it 1.918 r_mcangle_other 1.918 r_scbond_it 1.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.91 r_dihedral_angle_4_deg 13.062 r_dihedral_angle_3_deg 11.597 r_dihedral_angle_1_deg 6.568 r_long_range_B_refined 3.631 r_long_range_B_other 3.564 r_scangle_other 2.382 r_mcangle_it 1.918 r_mcangle_other 1.918 r_scbond_it 1.565 r_scbond_other 1.564 r_angle_refined_deg 1.508 r_mcbond_it 1.275 r_mcbond_other 1.272 r_angle_other_deg 1.006 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 5786 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing