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Single crystal serial study of the inhibition of laccases from Steccherinum murashkinskyi by chloride anions at sub-atomic resolution. First structure of the series with 15 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 NaCl.
Crystal Properties Matthews coefficient Solvent content 2.47 50.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.06 α = 90 b = 83.97 β = 90 c = 111.97 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 1.06 70 99.6 0.108 0.995 7.9 4.7 237855
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 1.06 1.09 99.7 0.645 0.762
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 1.06 67.18 226072 11783 99.6 0.12901 0.12801 0.1293 0.14862 0.1507 RANDOM 11.169
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] -1.53 0.1 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.3 r_dihedral_angle_4_deg 23.665 r_sphericity_free 22.007 r_sphericity_bonded 12.628 r_dihedral_angle_3_deg 10.784 r_dihedral_angle_1_deg 7.219 r_rigid_bond_restr 5.416 r_long_range_B_refined 2.935 r_long_range_B_other 2.386 r_scangle_other 2.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.3 r_dihedral_angle_4_deg 23.665 r_sphericity_free 22.007 r_sphericity_bonded 12.628 r_dihedral_angle_3_deg 10.784 r_dihedral_angle_1_deg 7.219 r_rigid_bond_restr 5.416 r_long_range_B_refined 2.935 r_long_range_B_other 2.386 r_scangle_other 2.197 r_angle_refined_deg 1.973 r_scbond_other 1.787 r_scbond_it 1.786 r_mcangle_it 1.498 r_mcangle_other 1.497 r_mcbond_it 1.171 r_mcbond_other 1.166 r_angle_other_deg 1.099 r_chiral_restr 0.145 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 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 853 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing