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Unspecific peroxygenase from Marasmius wettsteinii (MweUPO-1) in complex with dodecane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 15% PEG 4000, 200mM ammonium sulfate.
Soaking: 25mM dodecane, 16 hours, cryoprotected with 15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.56 51.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.283 α = 90 b = 76.283 β = 90 c = 186.687 γ = 90
Symmetry Space Group P 43 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 PILATUS 6M KB MIRRORS 2021-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.8 46.72 99.8 0.038 0.041 0.016 0.999 22.7 6.4 51958
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 1.8 1.84 99.9 0.644 0.7 0.269 0.919 2.2 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 46.72 49170 2664 99.66 0.17626 0.17396 0.1842 0.22033 0.2278 RANDOM 36.577
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 1.3 -2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.678 r_dihedral_angle_2_deg 8.459 r_long_range_B_refined 7.24 r_long_range_B_other 7.232 r_dihedral_angle_1_deg 6.564 r_scangle_other 5.976 r_mcangle_it 4.186 r_mcangle_other 4.185 r_scbond_it 4.177 r_scbond_other 4.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.678 r_dihedral_angle_2_deg 8.459 r_long_range_B_refined 7.24 r_long_range_B_other 7.232 r_dihedral_angle_1_deg 6.564 r_scangle_other 5.976 r_mcangle_it 4.186 r_mcangle_other 4.185 r_scbond_it 4.177 r_scbond_other 4.115 r_mcbond_it 3.162 r_mcbond_other 3.158 r_angle_refined_deg 1.491 r_angle_other_deg 0.521 r_chiral_restr 0.073 r_gen_planes_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_dihedral_angle_4_deg 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 3881 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing