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Unspecific peroxygenase from Marasmius wettsteinii (MweUPO-1) in complex with prednisone
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 14% PEG 4000, 200mM ammonium sulfate.
Soaking: 10mM prednisone, 5h30, cryoprotected with 15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.44 49.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.126 α = 90 b = 76.126 β = 90 c = 186.725 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 1.58 46.68 98 0.045 0.049 0.018 0.999 19.4 6.4 74091
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 1.58 1.61 99.6 0.457 0.495 0.187 0.969 3.1 6.7
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 1.58 46.68 70262 3655 97.2 0.1836 0.18186 0.1947 0.21842 0.2307 RANDOM 22.005
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] 0.65 0.65 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.547 r_dihedral_angle_2_deg 9.694 r_dihedral_angle_1_deg 6.331 r_long_range_B_refined 4.363 r_long_range_B_other 4.349 r_scangle_other 3.133 r_mcangle_other 2.053 r_mcangle_it 2.052 r_scbond_it 2.052 r_scbond_other 2.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.547 r_dihedral_angle_2_deg 9.694 r_dihedral_angle_1_deg 6.331 r_long_range_B_refined 4.363 r_long_range_B_other 4.349 r_scangle_other 3.133 r_mcangle_other 2.053 r_mcangle_it 2.052 r_scbond_it 2.052 r_scbond_other 2.052 r_angle_refined_deg 1.376 r_mcbond_it 1.358 r_mcbond_other 1.347 r_angle_other_deg 0.503 r_chiral_restr 0.067 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 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 3910 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing