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Complex structure of catalytic, small, and a partial electron transfer subunits from Burkholderia cepacia FAD glucose dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6A2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 5.6 293 tacsimate, PEG 3350, DDM, sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.5 64.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.015 α = 90 b = 71.797 β = 90 c = 114.221 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS3 6M 2016-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3 50 99.8 0.165 0.179 0.998 10.34 6.7 34334
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.08 0.732 0.7909999999999999 0.961
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 6A2U 3 49.88 32619 1725 99.8 0.27778 0.27531 0.2965 0.32335 0.3294 RANDOM 74.33
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] -7.01 -5.86 12.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.245 r_dihedral_angle_3_deg 20.743 r_dihedral_angle_4_deg 17.43 r_long_range_B_other 7.183 r_long_range_B_refined 7.182 r_dihedral_angle_1_deg 5.15 r_mcangle_it 4.808 r_mcangle_other 4.808 r_scangle_other 3.937 r_rigid_bond_restr 3.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.245 r_dihedral_angle_3_deg 20.743 r_dihedral_angle_4_deg 17.43 r_long_range_B_other 7.183 r_long_range_B_refined 7.182 r_dihedral_angle_1_deg 5.15 r_mcangle_it 4.808 r_mcangle_other 4.808 r_scangle_other 3.937 r_rigid_bond_restr 3.352 r_mcbond_it 2.93 r_mcbond_other 2.93 r_scbond_it 2.45 r_scbond_other 2.44 r_angle_refined_deg 1.135 r_angle_other_deg 1.021 r_chiral_restr 0.028 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_bond_other_d 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5935 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 103
Software Software Software Name Purpose XSCALE data scaling XDS data reduction REFMAC refinement MOLREP phasing