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Pyranose 2-oxidase from Trametes multicolor, L537G 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 2.55 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.54 α = 90 b = 103.18 β = 106.45 c = 169.34 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 2006-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.042 MAX II I911-2
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 2.1 40 99 0.066 17.2 4.4 321136 321136
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 2.1 2.2 94 0.262 6.2 3.3 39548
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 2.1 29.72 317871 317871 3262 99.07 0.15645 0.15645 0.15597 0.1684 0.20395 0.2147 RANDOM 31.659
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] -0.4 0.47 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.718 r_dihedral_angle_4_deg 14.923 r_dihedral_angle_3_deg 14.768 r_dihedral_angle_1_deg 7.09 r_scangle_it 4.507 r_scbond_it 3.013 r_mcangle_it 1.965 r_angle_refined_deg 1.863 r_mcbond_it 1.267 r_angle_other_deg 1.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.718 r_dihedral_angle_4_deg 14.923 r_dihedral_angle_3_deg 14.768 r_dihedral_angle_1_deg 7.09 r_scangle_it 4.507 r_scbond_it 3.013 r_mcangle_it 1.965 r_angle_refined_deg 1.863 r_mcbond_it 1.267 r_angle_other_deg 1.006 r_mcbond_other 0.313 r_xyhbond_nbd_other 0.263 r_nbd_refined 0.221 r_nbd_other 0.21 r_symmetry_vdw_other 0.19 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.158 r_symmetry_vdw_refined 0.146 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.14 r_nbtor_other 0.094 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36360 Nucleic Acid Atoms Solvent Atoms 1857 Heterogen Atoms 424
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing