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Pyranose 2-oxidase from Trametes multicolor, E542K mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IGO PDB ENTRY 2IGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 298 12-14(w/v)% monomethylether PEG 2000, 0.1M Mes, 50mM MgCl2, 25% glycerol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.56 52.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.863 α = 90 b = 103.746 β = 106.31 c = 169.333 γ = 90
Symmetry Space Group P 1 21 1
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 mirrors 2004-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.7 40 98.2 0.137 9.7 3.8 603616 603616
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.75 97.4 0.588 2.2 3.2 49624
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2IGO 1.7 40 597554 597554 6061 98.27 0.16601 0.16601 0.16569 0.1769 0.19787 0.2058 RANDOM 21.49
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] -0.12 0.34 0.36 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.524 r_dihedral_angle_4_deg 14.213 r_dihedral_angle_3_deg 13.244 r_dihedral_angle_1_deg 6.801 r_scangle_it 4.205 r_scbond_it 3.048 r_angle_refined_deg 1.887 r_mcangle_it 1.84 r_mcbond_it 1.561 r_angle_other_deg 1.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.524 r_dihedral_angle_4_deg 14.213 r_dihedral_angle_3_deg 13.244 r_dihedral_angle_1_deg 6.801 r_scangle_it 4.205 r_scbond_it 3.048 r_angle_refined_deg 1.887 r_mcangle_it 1.84 r_mcbond_it 1.561 r_angle_other_deg 1.008 r_mcbond_other 0.384 r_symmetry_vdw_refined 0.337 r_symmetry_vdw_other 0.274 r_nbd_refined 0.236 r_xyhbond_nbd_other 0.22 r_nbd_other 0.213 r_nbtor_refined 0.185 r_chiral_restr 0.166 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.13 r_nbtor_other 0.093 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36392 Nucleic Acid Atoms Solvent Atoms 2546 Heterogen Atoms 424
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing