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The study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi.The third structure of the series with total exposition time 63 min.
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, 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 50.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.39 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 0.048 0.999 19.49 3.1 116957 -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 98.5 0.313 0.896 4.66 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5E9N 1.35 67.52 111101 5856 98.81 0.1343 0.13334 0.1347 0.15236 0.1535 RANDOM 10.794
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 0.01 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.604 r_dihedral_angle_4_deg 21.367 r_dihedral_angle_3_deg 11.338 r_dihedral_angle_1_deg 7.169 r_long_range_B_refined 4.583 r_sphericity_bonded 4.162 r_long_range_B_other 3.95 r_scangle_other 2.325 r_angle_refined_deg 2.023 r_scbond_it 1.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.604 r_dihedral_angle_4_deg 21.367 r_dihedral_angle_3_deg 11.338 r_dihedral_angle_1_deg 7.169 r_long_range_B_refined 4.583 r_sphericity_bonded 4.162 r_long_range_B_other 3.95 r_scangle_other 2.325 r_angle_refined_deg 2.023 r_scbond_it 1.653 r_mcangle_it 1.581 r_scbond_other 1.565 r_mcangle_other 1.506 r_mcbond_it 1.074 r_mcbond_other 1.024 r_angle_other_deg 0.916 r_chiral_restr 0.134 r_bond_refined_d 0.021 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 682 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing