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Crystal structure of 5-hydroxymethylfurfural oxidase (HMFO) in the oxidized state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JBV PDB ENTRY 2JBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 16-22% W/V PEG3350, 200 MM MAGNESIUM FORMATE
Crystal Properties Matthews coefficient Solvent content 1.92 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.964 α = 90 b = 120.907 β = 91.39 c = 72.322 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 PIXEL DECTRIS PILATUS 6M 2014-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) PETRA III, EMBL c/o DESY P13 (MX1)
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 1.9 50 99.9 0.15 9 6.9 67679
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 1.9 1.94 99.9 0.97 0.85 6.9
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2JBV 1.9 72.3 64121 3218 99.79 0.18076 0.17805 0.1907 0.23609 0.2456 RANDOM 24.92
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] 3.77 -0.11 -0.9 -2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.915 r_dihedral_angle_4_deg 19.084 r_dihedral_angle_3_deg 15.917 r_dihedral_angle_1_deg 7.214 r_mcangle_it 2.648 r_scbond_it 2.44 r_angle_refined_deg 1.858 r_mcbond_it 1.853 r_mcbond_other 1.853 r_angle_other_deg 0.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.915 r_dihedral_angle_4_deg 19.084 r_dihedral_angle_3_deg 15.917 r_dihedral_angle_1_deg 7.214 r_mcangle_it 2.648 r_scbond_it 2.44 r_angle_refined_deg 1.858 r_mcbond_it 1.853 r_mcbond_other 1.853 r_angle_other_deg 0.915 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7861 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling BALBES phasing