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The Native Crystal Structure of the Primary Hexose Oxidase (Dbv29) in Antibiotic A40926 Biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IPI PDB ENTRY 2IPI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 PROTEIN WAS CRYSTALLIZED FROM 30% PEG 550 MME, 0.05M CALCIUM CHLORIDE, 0.1M BIS TRIS, PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.092 α = 90 b = 66.092 β = 90 c = 790.462 γ = 120
Symmetry Space Group P 61 2 2
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 ADSC QUANTUM 210 2007-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 NSRRC BL13C1
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 3.21 30 95.7 0.08 24.8 9.7 17824 2
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 3.21 3.32 92 0.16 17 9.8
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 2IPI 3.21 29.54 16838 869 96.1 0.24 0.237 0.2367 0.291 0.2253 RANDOM 28.94
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] 0.96 0.48 0.96 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.188 r_dihedral_angle_3_deg 15.69 r_dihedral_angle_4_deg 11.98 r_dihedral_angle_1_deg 4.179 r_angle_refined_deg 0.837 r_nbtor_refined 0.299 r_scangle_it 0.295 r_mcangle_it 0.225 r_scbond_it 0.163 r_nbd_refined 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.188 r_dihedral_angle_3_deg 15.69 r_dihedral_angle_4_deg 11.98 r_dihedral_angle_1_deg 4.179 r_angle_refined_deg 0.837 r_nbtor_refined 0.299 r_scangle_it 0.295 r_mcangle_it 0.225 r_scbond_it 0.163 r_nbd_refined 0.152 r_mcbond_it 0.125 r_xyhbond_nbd_refined 0.098 r_symmetry_vdw_refined 0.098 r_symmetry_hbond_refined 0.085 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 7710 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing