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The study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi.The 9-th structure of the series with total exposition time 243 min.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 294 Protein solution (12mg/ml, 002M K-phosphate buffer, pH 6.5). Reservoir solution
(0.1M citrate-phosphate buffer pH4.0, 0.2M ammonium acetat, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.51 50.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.38 α = 90 b = 84.41 β = 90 c = 112.52 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 1.35 67.52 98.7 0.045 0.999 20.51 3.1 116868 -3
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 1.35 1.4 98.3 0.282 0.912 5.14 3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5MEW 1.35 67.52 111021 5847 98.73 0.13134 0.1305 0.14686 0.1375 RANDOM 10.984
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] 0.09 0.02 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.01 r_dihedral_angle_4_deg 21.084 r_dihedral_angle_3_deg 11.148 r_dihedral_angle_1_deg 7.194 r_sphericity_bonded 6.472 r_long_range_B_refined 5.018 r_long_range_B_other 4.275 r_scangle_other 2.284 r_angle_refined_deg 1.962 r_scbond_it 1.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.01 r_dihedral_angle_4_deg 21.084 r_dihedral_angle_3_deg 11.148 r_dihedral_angle_1_deg 7.194 r_sphericity_bonded 6.472 r_long_range_B_refined 5.018 r_long_range_B_other 4.275 r_scangle_other 2.284 r_angle_refined_deg 1.962 r_scbond_it 1.629 r_mcangle_it 1.571 r_scbond_other 1.542 r_mcangle_other 1.483 r_mcbond_it 1.046 r_mcbond_other 0.998 r_angle_other_deg 0.892 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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 759 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing