☰ Navigation Tabs
Ligninolytic manganese peroxidase Ape-MnP1 from Agaricales mushrooms
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 2.24 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.623 α = 90 b = 39.63 β = 101.231 c = 63.493 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 0.97900 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 1.6 48.781 98.3 0.045 0.061 0.041 0.998 14.1 3.3 39894
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 1.6 1.63 98.3 0.475 0.569 0.428 0.801 2.4 3.3
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 1.6 48.781 39881 1981 97.978 0.153 0.1508 0.1504 0.1864 0.1865 16.934
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] -0.551 0.541 0.038 0.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.026 r_dihedral_angle_3_deg 11.31 r_dihedral_angle_2_deg 6.832 r_dihedral_angle_1_deg 5.644 r_lrange_it 5.235 r_lrange_other 5.199 r_scangle_it 4.665 r_scangle_other 4.664 r_scbond_it 3.128 r_scbond_other 3.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.026 r_dihedral_angle_3_deg 11.31 r_dihedral_angle_2_deg 6.832 r_dihedral_angle_1_deg 5.644 r_lrange_it 5.235 r_lrange_other 5.199 r_scangle_it 4.665 r_scangle_other 4.664 r_scbond_it 3.128 r_scbond_other 3.127 r_mcangle_it 2.211 r_mcangle_other 2.21 r_angle_refined_deg 1.876 r_mcbond_it 1.523 r_mcbond_other 1.517 r_angle_other_deg 0.628 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.223 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.177 r_nbd_other 0.124 r_symmetry_xyhbond_nbd_refined 0.1 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.08 r_metal_ion_refined 0.058 r_symmetry_nbd_refined 0.028 r_gen_planes_refined 0.012 r_gen_planes_other 0.012 r_bond_refined_d 0.011 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2428 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing