☰ Navigation Tabs
Crystal structure of PETase P181A mutant from Ideonella sakaiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Tris, PEG 3000, NaCl
Crystal Properties Matthews coefficient Solvent content 1.92 36.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.479 α = 90 b = 50.937 β = 92.58 c = 41.262 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 270 2017-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.72 50 98.8 0.047 27.31 3.2 25150
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 0.227
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 5XJH 1.72 24.22 23905 1245 98.48 0.20916 0.2064 0.2182 0.26154 0.2682 RANDOM 24.972
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] -0.47 -2.25 -0.77 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.557 r_dihedral_angle_4_deg 18.435 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_1_deg 6.993 r_long_range_B_refined 5.335 r_long_range_B_other 5.33 r_scangle_other 3.817 r_mcangle_it 3.116 r_mcangle_other 3.115 r_scbond_it 2.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.557 r_dihedral_angle_4_deg 18.435 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_1_deg 6.993 r_long_range_B_refined 5.335 r_long_range_B_other 5.33 r_scangle_other 3.817 r_mcangle_it 3.116 r_mcangle_other 3.115 r_scbond_it 2.538 r_scbond_other 2.537 r_mcbond_it 2.179 r_mcbond_other 2.179 r_angle_refined_deg 1.64 r_angle_other_deg 1.387 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 1916 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 data collection Coot model building MOLREP phasing