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Ligninolytic manganese peroxidase Cst-MnP1 from Agaricales mushrooms in complex with a manganese ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 20% PEG 8000, 0,1 M Tris-HCl, pH 7, 0,3M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.16 43.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.79 α = 90 b = 56.64 β = 90 c = 109.51 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 110 PIXEL DECTRIS PILATUS 6M 2019-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 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 1.5 56.64 99.9 0.114 0.138 0.076 0.996 8.3 5.8 48414
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 1.5 1.53 99.8 1.147 1.389 0.773 0.638 1.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 54.755 48336 2432 99.855 0.164 0.1632 0.1678 0.1888 0.1931 16.86
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] 2.362 -1.688 -0.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.696 r_dihedral_angle_3_deg 11.107 r_dihedral_angle_2_deg 6.737 r_dihedral_angle_1_deg 5.881 r_lrange_it 4.429 r_lrange_other 4.429 r_scangle_it 3.422 r_scangle_other 3.422 r_mcangle_other 2.388 r_mcangle_it 2.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.696 r_dihedral_angle_3_deg 11.107 r_dihedral_angle_2_deg 6.737 r_dihedral_angle_1_deg 5.881 r_lrange_it 4.429 r_lrange_other 4.429 r_scangle_it 3.422 r_scangle_other 3.422 r_mcangle_other 2.388 r_mcangle_it 2.387 r_scbond_it 2.344 r_scbond_other 2.341 r_angle_refined_deg 1.863 r_mcbond_it 1.629 r_mcbond_other 1.628 r_angle_other_deg 0.671 r_symmetry_nbd_refined 0.307 r_nbd_other 0.28 r_nbd_refined 0.24 r_symmetry_xyhbond_nbd_refined 0.221 r_xyhbond_nbd_refined 0.204 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.18 r_chiral_restr 0.093 r_metal_ion_refined 0.086 r_symmetry_nbtor_other 0.078 r_chiral_restr_other 0.04 r_gen_planes_refined 0.011 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2415 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing