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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. Twentieth structure of the series with 4065 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 2.51 51.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.43 α = 90 b = 84.3 β = 90 c = 112.67 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 1.07 70 99.7 0.083 0.996 9.7 4.6 235403
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 1.07 1.1 99.8 0.839 0.662 1.8
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 1.07 67.5 223764 11639 99.7 0.12709 0.12628 0.1268 0.14252 0.1429 RANDOM 13.576
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] -1.47 -0.24 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.219 r_dihedral_angle_4_deg 21.113 r_dihedral_angle_3_deg 10.553 r_dihedral_angle_1_deg 6.885 r_long_range_B_refined 3.061 r_long_range_B_other 2.59 r_scangle_other 2.465 r_scbond_other 1.931 r_scbond_it 1.927 r_angle_refined_deg 1.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.219 r_dihedral_angle_4_deg 21.113 r_dihedral_angle_3_deg 10.553 r_dihedral_angle_1_deg 6.885 r_long_range_B_refined 3.061 r_long_range_B_other 2.59 r_scangle_other 2.465 r_scbond_other 1.931 r_scbond_it 1.927 r_angle_refined_deg 1.843 r_mcangle_it 1.648 r_mcangle_other 1.644 r_mcbond_it 1.281 r_mcbond_other 1.275 r_angle_other_deg 1.063 r_chiral_restr 0.132 r_bond_refined_d 0.019 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3765 Nucleic Acid Atoms Solvent Atoms 739 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing