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Crystal structure of a novel PET hydrolase R103G/S131A mutant in complex with pNP from Ideonella sakaiensis 201-F6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WFI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 Ammonium Sulfate, NaCl, HEPES
Crystal Properties Matthews coefficient Solvent content 2.02 39.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.784 α = 90 b = 51.532 β = 90 c = 84.373 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX300-HS 2017-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.9998 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.2 25 99.8 0.05 0.053 0.019 10 8 69716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.24 98.9 0.212 0.228 0.081 0.982 7.6
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 4WFI 1.2 25 66256 3391 99.59 0.0997 0.0984 0.1061 0.1246 0.1301 RANDOM 10.757
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] -0.3 0.29 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.729 r_sphericity_free 26.525 r_dihedral_angle_4_deg 17.151 r_dihedral_angle_3_deg 10.441 r_sphericity_bonded 9.793 r_rigid_bond_restr 7.103 r_dihedral_angle_1_deg 6.596 r_angle_refined_deg 1.489 r_angle_other_deg 0.821 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.729 r_sphericity_free 26.525 r_dihedral_angle_4_deg 17.151 r_dihedral_angle_3_deg 10.441 r_sphericity_bonded 9.793 r_rigid_bond_restr 7.103 r_dihedral_angle_1_deg 6.596 r_angle_refined_deg 1.489 r_angle_other_deg 0.821 r_chiral_restr 0.106 r_gen_planes_refined 0.014 r_bond_refined_d 0.011 r_gen_planes_other 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1912 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing HKL data scaling