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Crystal Structure of PQQ-dependent sugar dehydrogenase apo-form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ISM
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 4.76 74.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.74 α = 90 b = 177.74 β = 90 c = 89.937 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 2.39 50 99.9 28570 28570
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 2ISM 2.39 40.13 28369 27108 1448 99.62 0.20167 0.20068 0.2199 0.21989 0.2317 RANDOM 38.722
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] -3.31 -3.31 6.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.904 r_dihedral_angle_4_deg 21.033 r_dihedral_angle_3_deg 18.439 r_dihedral_angle_1_deg 6.828 r_scangle_it 2.747 r_scbond_it 1.776 r_angle_refined_deg 1.519 r_mcangle_it 1.494 r_mcbond_it 0.832 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.904 r_dihedral_angle_4_deg 21.033 r_dihedral_angle_3_deg 18.439 r_dihedral_angle_1_deg 6.828 r_scangle_it 2.747 r_scbond_it 1.776 r_angle_refined_deg 1.519 r_mcangle_it 1.494 r_mcbond_it 0.832 r_nbtor_refined 0.311 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.109 r_chiral_restr 0.104 r_metal_ion_refined 0.078 r_bond_refined_d 0.012 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 110 Heterogen Atoms 47
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