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PETase from Ideonella sakaiensis without ligand
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 5 293 1 ul protein (10 mg/ml, 20 mM TRIS pH 7.5, 150 mM NaCl) + 1 ul reservoir (0.1 M sodium citrate or sodium acetate pH 5.0, 15% (v/v) PEG8000, 0.5 M lithium sulfate)
Crystal Properties Matthews coefficient Solvent content 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.121 α = 90 b = 78.769 β = 92.56 c = 140.121 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 PILATUS 6M mirror 2017-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9799 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 2 100 97.1 0.131 0.151 0.991 8.4 4.2 73090 27.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.12 95.3 0.719 0.838 0.62 1.6 3.6
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 48.73 69684 3607 97.43 0.21578 0.21347 0.2212 0.26091 0.2643 RANDOM 23.386
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] 1.3 0.33 -2.11 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.802 r_dihedral_angle_4_deg 17.402 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_1_deg 7.406 r_long_range_B_refined 4.467 r_long_range_B_other 4.401 r_angle_refined_deg 1.817 r_angle_other_deg 1.052 r_scangle_other 0.826 r_mcangle_it 0.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.802 r_dihedral_angle_4_deg 17.402 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_1_deg 7.406 r_long_range_B_refined 4.467 r_long_range_B_other 4.401 r_angle_refined_deg 1.817 r_angle_other_deg 1.052 r_scangle_other 0.826 r_mcangle_it 0.658 r_mcangle_other 0.658 r_scbond_it 0.587 r_scbond_other 0.517 r_mcbond_it 0.385 r_mcbond_other 0.385 r_chiral_restr 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 7689 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing