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Structure of Polyphenol Oxidase (mutant G292N) from Thermothelomyces thermophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Moprheus buffer 3, amino acids mix, MPD, PEG1000, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.404 α = 90 b = 97.177 β = 90 c = 46.998 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER X 16M 2019-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.98012 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.53 43.24 86.3 0.999 12.4 13.3 30047
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.554 1.719 0.605
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 4J3Q 1.53 43.24 28590 1478 49.67 0.15989 0.15743 0.1681 0.20659 0.2124 RANDOM 21.138
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] -0.31 0.01 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.209 r_dihedral_angle_4_deg 21.799 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 6.678 r_long_range_B_refined 5.55 r_long_range_B_other 5.445 r_scangle_other 3.678 r_mcangle_other 2.801 r_mcangle_it 2.8 r_scbond_it 2.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.209 r_dihedral_angle_4_deg 21.799 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 6.678 r_long_range_B_refined 5.55 r_long_range_B_other 5.445 r_scangle_other 3.678 r_mcangle_other 2.801 r_mcangle_it 2.8 r_scbond_it 2.315 r_scbond_other 2.315 r_mcbond_it 1.848 r_mcbond_other 1.822 r_angle_refined_deg 1.679 r_angle_other_deg 1.368 r_chiral_restr 0.083 r_bond_refined_d 0.01 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 2964 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing