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Xylooligosaccharide oxidase from Myceliophthora thermophila C1 in complex with Xylobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 15-18% PEG3350, 0.1 M MES buffer, 0.2 M ammonium chloride
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.591 α = 90 b = 59.226 β = 90.76 c = 68.502 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH 2015-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 53.4 99.4 0.066 11.4 3.6 45931 11.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 90 0.274 3.3 2.9
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 FOURIER SYNTHESIS THROUGHOUT 5K8E 1.8 53.4 43668 2252 99.38 0.15379 0.1523 0.1638 0.18371 0.19 RANDOM 17.848
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] 0.2 -0.3 0.14 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.806 r_dihedral_angle_4_deg 15.047 r_dihedral_angle_3_deg 11.484 r_dihedral_angle_1_deg 6.914 r_long_range_B_refined 4.932 r_long_range_B_other 4.73 r_scangle_other 2.206 r_angle_refined_deg 1.454 r_scbond_it 1.355 r_scbond_other 1.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.806 r_dihedral_angle_4_deg 15.047 r_dihedral_angle_3_deg 11.484 r_dihedral_angle_1_deg 6.914 r_long_range_B_refined 4.932 r_long_range_B_other 4.73 r_scangle_other 2.206 r_angle_refined_deg 1.454 r_scbond_it 1.355 r_scbond_other 1.354 r_mcangle_other 1.191 r_mcangle_it 1.19 r_angle_other_deg 0.799 r_mcbond_it 0.678 r_mcbond_other 0.678 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3673 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing