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Crystal structure of glucose dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 PEG4000
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.364 α = 90 b = 88.612 β = 106.422 c = 80.77 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 2017-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.000 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 1.329 77.475 99.8 0.052 0.94 23.3 6.4 170679
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.33 1.35 0.383 0.713
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2g8s 1.329 77.475 170646 8519 99.408 0.167 0.1663 0.1662 0.1813 0.1813 15.871
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] -0.265 -0.256 0.819 -0.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.056 r_dihedral_angle_4_deg 14.269 r_dihedral_angle_3_deg 12.786 r_dihedral_angle_1_deg 6.881 r_lrange_it 4.972 r_lrange_other 4.777 r_scangle_it 4.095 r_scangle_other 4.094 r_scbond_it 3.045 r_scbond_other 3.045
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.056 r_dihedral_angle_4_deg 14.269 r_dihedral_angle_3_deg 12.786 r_dihedral_angle_1_deg 6.881 r_lrange_it 4.972 r_lrange_other 4.777 r_scangle_it 4.095 r_scangle_other 4.094 r_scbond_it 3.045 r_scbond_other 3.045 r_mcangle_it 2.489 r_mcangle_other 2.488 r_angle_other_deg 2.309 r_mcbond_it 1.823 r_mcbond_other 1.818 r_angle_refined_deg 1.768 r_symmetry_xyhbond_nbd_refined 0.231 r_symmetry_nbd_other 0.217 r_xyhbond_nbd_refined 0.206 r_nbd_refined 0.203 r_nbd_other 0.195 r_nbtor_refined 0.177 r_chiral_restr 0.124 r_symmetry_nbd_refined 0.117 r_symmetry_nbtor_other 0.093 r_metal_ion_refined 0.072 r_symmetry_xyhbond_nbd_other 0.058 r_bond_other_d 0.035 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5337 Nucleic Acid Atoms Solvent Atoms 994 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing