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Crystal Structure of PQQ-dependent sugar dehydrogenase holo-form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop 6.6 293 ammonium sulfate, pH 6.6, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.73 73.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.344 α = 90 b = 177.344 β = 90 c = 89.743 γ = 90
Symmetry Space Group I 41 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 270 2009-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 50 99.9 24995 24995 41.7
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 (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 3A9G 2.5 44.34 24982 23709 1272 99.87 0.20225 0.20069 0.2177 0.2313 0.2242 RANDOM 39.697
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] -4.24 -4.24 8.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.108 r_dihedral_angle_4_deg 21.527 r_dihedral_angle_3_deg 18.967 r_dihedral_angle_1_deg 6.922 r_scangle_it 2.663 r_scbond_it 1.708 r_angle_refined_deg 1.592 r_mcangle_it 1.466 r_mcbond_it 0.83 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.108 r_dihedral_angle_4_deg 21.527 r_dihedral_angle_3_deg 18.967 r_dihedral_angle_1_deg 6.922 r_scangle_it 2.663 r_scbond_it 1.708 r_angle_refined_deg 1.592 r_mcangle_it 1.466 r_mcbond_it 0.83 r_nbtor_refined 0.318 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.104 r_metal_ion_refined 0.049 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2571 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 71
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement