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Ligninolytic manganese peroxidase Ape-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 4.2 295 30% P2000 MME, 0,1 M sodium citrate, pH 4.2
Crystal Properties Matthews coefficient Solvent content 2.23 44.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.63 α = 90 b = 39.811 β = 101.5 c = 63.56 γ = 90
Symmetry Space Group P 1 21 1
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 2018-10-18 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 1.24 62.29 95.2 0.048 0.068 0.048 0.999 10 3.2 81601
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 1.24 1.27 94.9 0.497 0.7 0.493 0.539 1.7 3.2
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 1.247 62.284 81594 4019 95.081 0.179 0.1775 0.1784 0.1989 0.1994 12.623
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] -0.048 0.415 -0.581 0.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.801 r_dihedral_angle_3_deg 11.853 r_dihedral_angle_1_deg 5.939 r_dihedral_angle_2_deg 5.669 r_lrange_it 3.91 r_lrange_other 3.889 r_scangle_it 3.421 r_scangle_other 3.42 r_scbond_other 2.379 r_scbond_it 2.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.801 r_dihedral_angle_3_deg 11.853 r_dihedral_angle_1_deg 5.939 r_dihedral_angle_2_deg 5.669 r_lrange_it 3.91 r_lrange_other 3.889 r_scangle_it 3.421 r_scangle_other 3.42 r_scbond_other 2.379 r_scbond_it 2.377 r_angle_refined_deg 2.059 r_mcangle_other 1.869 r_mcangle_it 1.866 r_angle_other_deg 1.362 r_mcbond_it 1.271 r_mcbond_other 1.269 r_xyhbond_nbd_refined 0.241 r_nbd_refined 0.229 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.179 r_nbd_other 0.156 r_chiral_restr 0.105 r_symmetry_xyhbond_nbd_refined 0.084 r_symmetry_nbtor_other 0.079 r_metal_ion_refined 0.067 r_symmetry_nbd_refined 0.063 r_gen_planes_refined 0.015 r_bond_refined_d 0.013 r_gen_planes_other 0.013 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2450 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing