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Single crystal serial study of the inhibition of laccases from Steccherinum murashkinskyi by fluoride anions at sub-atomic resolution. Third structure of the series with 800 KGy dose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E9N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4 294 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION (12MG/ML, 20 MM K-PHOSPHATE BUFFER, PH 6.5) RESERVOIR SOLUTION (0.1 M CITRATE-PHOSPHATE BUFFER PH 4.0, 0.2 M AMMONIUM ACETATE, 25% PEG 4000). Before collecting the diffraction data, the crystal was soaked in reservoir solution containing 0.1 M NaF.
Crystal Properties Matthews coefficient Solvent content 2.49 50.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.18 α = 90 b = 84.2 β = 90 c = 112.22 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 100 PIXEL DECTRIS PILATUS 6M 2017-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.886 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 0.95 70 97.2 0.077 0.996 11.6 4.4 323608
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 0.97 82.3 0.698 0.716 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5E9N 0.95 67.35 307589 16019 97.17 0.10616 0.10552 0.1078 0.11854 0.1205 RANDOM 12.604
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] -0.35 -0.38 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_4_deg 22.595 r_sphericity_free 18.027 r_dihedral_angle_3_deg 10.958 r_sphericity_bonded 8.825 r_dihedral_angle_1_deg 7.152 r_rigid_bond_restr 4.094 r_long_range_B_refined 2.697 r_long_range_B_other 2.197 r_scangle_other 2.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_4_deg 22.595 r_sphericity_free 18.027 r_dihedral_angle_3_deg 10.958 r_sphericity_bonded 8.825 r_dihedral_angle_1_deg 7.152 r_rigid_bond_restr 4.094 r_long_range_B_refined 2.697 r_long_range_B_other 2.197 r_scangle_other 2.024 r_angle_refined_deg 1.806 r_scbond_other 1.584 r_scbond_it 1.583 r_mcangle_other 1.314 r_mcangle_it 1.312 r_angle_other_deg 1.048 r_mcbond_it 0.99 r_mcbond_other 0.99 r_chiral_restr 0.123 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3765 Nucleic Acid Atoms Solvent Atoms 974 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing