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Crystal structure of Aspergillus flavus FAD glucose dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CF3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M BisTris, 20-25 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.95 36.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.907 α = 90 b = 64.359 β = 101.43 c = 76.166 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 CCD ADSC QUANTUM 315r 2014-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.77 50 99 0.071 15.2 3.2 45130
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 1.77 1.8 93.4 0.462 2.4 2.4 2102
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 1CF3 1.78 48.75 42833 2279 98.48 0.1556 0.1533 0.1637 0.199 0.2061 RANDOM 23.958
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.129 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 16.096 r_dihedral_angle_1_deg 8.011 r_angle_refined_deg 1.028 r_angle_other_deg 0.626 r_chiral_restr 0.071 r_gen_planes_refined 0.015 r_bond_refined_d 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.129 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 16.096 r_dihedral_angle_1_deg 8.011 r_angle_refined_deg 1.028 r_angle_other_deg 0.626 r_chiral_restr 0.071 r_gen_planes_refined 0.015 r_bond_refined_d 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4332 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement SCALEPACK data reduction PDB_EXTRACT data extraction HKL-2000 data scaling PHENIX phasing