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Single crystal serial study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi at sub-atomic resolution. Second structure of the series with 165 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).
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.233 α = 90 b = 84.115 β = 90 c = 112.336 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 0.97 70 99.6 0.071 0.997 11.2 4.5 312181
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 0.97 1 98.5 0.615 0.736 1.94
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 0.97 67.33 296484 15792 99.63 0.10878 0.10802 0.1099 0.12311 0.1247 RANDOM 12.834
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] -0.64 -0.24 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.12 r_dihedral_angle_4_deg 22.179 r_sphericity_free 19.654 r_dihedral_angle_3_deg 10.672 r_sphericity_bonded 10.28 r_dihedral_angle_1_deg 7.163 r_rigid_bond_restr 4.038 r_long_range_B_refined 3.021 r_long_range_B_other 2.182 r_scangle_other 2.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.12 r_dihedral_angle_4_deg 22.179 r_sphericity_free 19.654 r_dihedral_angle_3_deg 10.672 r_sphericity_bonded 10.28 r_dihedral_angle_1_deg 7.163 r_rigid_bond_restr 4.038 r_long_range_B_refined 3.021 r_long_range_B_other 2.182 r_scangle_other 2.072 r_angle_refined_deg 1.839 r_scbond_other 1.577 r_scbond_it 1.576 r_mcangle_it 1.373 r_mcangle_other 1.369 r_angle_other_deg 1.037 r_mcbond_it 0.944 r_mcbond_other 0.94 r_chiral_restr 0.124 r_bond_refined_d 0.015 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 985 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing