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Crystal Structure of Pyranose 2-Oxidase from the White-Rot Fungus Peniophora sp.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG 6000, MES, tributyl phosphine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.879 α = 90 b = 103.596 β = 105.25 c = 169.169 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 MARRESEARCH N2 cooled fixed-exit
Si(111) monochromator Dynamically bendable mirror 2003-06-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97934, 0.97950, 0.93926 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.35 20 96.1 0.092 0.066 8.42 2 228044 228044 3.99 3.99 33.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.35 2.42 94.9 0.295 0.21 3.99 2 35967
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 MAD THROUGHOUT 2.35 19.7 3.99 3.99 228316 219141 9088 99.96 0.17604 0.17604 0.17398 0.196 0.22575 0.2308 RANDOM 20.96
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] -0.77 -1.04 -1.85 2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.809 r_scangle_it 3.903 r_scbond_it 2.572 r_angle_refined_deg 1.45 r_mcangle_it 1.436 r_mcbond_it 0.764 r_symmetry_hbond_refined 0.234 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.809 r_scangle_it 3.903 r_scbond_it 2.572 r_angle_refined_deg 1.45 r_mcangle_it 1.436 r_mcbond_it 0.764 r_symmetry_hbond_refined 0.234 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.101 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36392 Nucleic Acid Atoms Solvent Atoms 2154 Heterogen Atoms 424
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MLPHARE phasing