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Structure of a glucose dehydrogenase T277F mutant in complex with D-glucose and NAADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 PEG 400, 1,2-propanediol, HEPES, NAADP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.68 54.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.91 α = 90 b = 92.331 β = 91.12 c = 120.47 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 270 2013-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 2.33 50 99.9 75199 75199
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.33 2.37 99.9
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 (All) 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 3wid 2.33 28.01 75199 74890 3752 98.48 0.1936 0.1936 0.1909 0.1995 0.2436 0.2464 RANDOM 49.6365
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] -1.96 -0.14 2.42 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.112 r_dihedral_angle_4_deg 22.615 r_dihedral_angle_3_deg 18.442 r_dihedral_angle_1_deg 7.034 r_mcangle_it 5.699 r_mcbond_it 4.034 r_mcbond_other 4.034 r_angle_refined_deg 1.931 r_angle_other_deg 0.934 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.112 r_dihedral_angle_4_deg 22.615 r_dihedral_angle_3_deg 18.442 r_dihedral_angle_1_deg 7.034 r_mcangle_it 5.699 r_mcbond_it 4.034 r_mcbond_other 4.034 r_angle_refined_deg 1.931 r_angle_other_deg 0.934 r_chiral_restr 0.109 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11308 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 248
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection