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Structural study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi. First structure of the series with 3 min total X-ray exposition time.
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, HANGING DROP 4 294 Protein solution (12mg/ml, 0.02M K-phosphate buffer, pH 6.5). Reservoir solution (0.1M citrate-phosphate buffer pH 4.0, 0.2M ammonium acetate, 25% PEG 4000).
Crystal Properties Matthews coefficient Solvent content 2.51 50.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.37 α = 90 b = 84.39 β = 90 c = 112.48 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 CCD MAR CCD 165 mm 2009-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81230 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 67.6 97.6 0.062 0.998 14.85 3.1 84461 -3 17.665
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.65 94.1 0.352 0.842 3.25
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 1.5 67.57 80220 4241 98 0.1405 0.13938 0.1413 0.16147 0.163 RANDOM 11.555
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] 0.13 0.02 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.72 r_dihedral_angle_4_deg 19.94 r_dihedral_angle_3_deg 11.272 r_dihedral_angle_1_deg 7.078 r_sphericity_bonded 5.726 r_long_range_B_refined 4.509 r_long_range_B_other 3.815 r_scangle_other 2.02 r_angle_refined_deg 1.826 r_mcangle_it 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.72 r_dihedral_angle_4_deg 19.94 r_dihedral_angle_3_deg 11.272 r_dihedral_angle_1_deg 7.078 r_sphericity_bonded 5.726 r_long_range_B_refined 4.509 r_long_range_B_other 3.815 r_scangle_other 2.02 r_angle_refined_deg 1.826 r_mcangle_it 1.45 r_scbond_it 1.444 r_mcangle_other 1.362 r_scbond_other 1.348 r_mcbond_it 0.962 r_mcbond_other 0.909 r_angle_other_deg 0.882 r_chiral_restr 0.124 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3775 Nucleic Acid Atoms Solvent Atoms 662 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing XSCALE data reduction