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The study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi.The 8-th structure of the series with total exposition time 213 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 = 112.51 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 98.8 0.044 0.999 20.84 3.1 116915 -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 98.4 0.271 0.918 5.34 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 111057 5858 98.78 0.13121 0.13034 0.14728 0.1401 RANDOM 10.9
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] 0.1 0.02 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.156 r_dihedral_angle_4_deg 21.38 r_dihedral_angle_3_deg 10.974 r_dihedral_angle_1_deg 7.221 r_sphericity_bonded 6.183 r_long_range_B_refined 4.894 r_long_range_B_other 4.167 r_scangle_other 2.285 r_angle_refined_deg 1.949 r_scbond_it 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.156 r_dihedral_angle_4_deg 21.38 r_dihedral_angle_3_deg 10.974 r_dihedral_angle_1_deg 7.221 r_sphericity_bonded 6.183 r_long_range_B_refined 4.894 r_long_range_B_other 4.167 r_scangle_other 2.285 r_angle_refined_deg 1.949 r_scbond_it 1.62 r_mcangle_it 1.551 r_scbond_other 1.534 r_mcangle_other 1.466 r_mcbond_it 1.04 r_mcbond_other 0.99 r_angle_other_deg 0.901 r_chiral_restr 0.132 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 757 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing