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Crystal structure of the soluble Aldose sugar dehydrogenase (Asd) from Escherichia coli in the apo-form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.2 289 18 % PEG 6000, 100 mM CHES, 100 mM sodium chloride, 1 mM calcium chloride, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.22 44.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.829 α = 90 b = 113.475 β = 90.03 c = 75.372 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 315 2004-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97935 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.315 75.378 72.2 0.057 0.057 6.9 3.3 162184 162184 0.2 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.31 1.38 10.9 10.9 0.386 0.386 1.9 1.7
Refinement Statistics Diffraction ID Structure Solution Method 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) Mean Isotropic B X-RAY DIFFRACTION SAD 1.5 7.96 117547 117547 97142 94.15 0.149 0.148 0.149 0.1472 0.183 12.384
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.273 r_dihedral_angle_4_deg 15.992 r_dihedral_angle_3_deg 12.659 r_dihedral_angle_1_deg 6.184 r_sphericity_free 2.599 r_scangle_it 2.312 r_scbond_it 1.624 r_sphericity_bonded 1.595 r_angle_refined_deg 1.215 r_mcangle_it 1.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.273 r_dihedral_angle_4_deg 15.992 r_dihedral_angle_3_deg 12.659 r_dihedral_angle_1_deg 6.184 r_sphericity_free 2.599 r_scangle_it 2.312 r_scbond_it 1.624 r_sphericity_bonded 1.595 r_angle_refined_deg 1.215 r_mcangle_it 1.125 r_rigid_bond_restr 0.927 r_mcbond_it 0.782 r_nbtor_refined 0.32 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.163 r_symmetry_vdw_refined 0.149 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.086 r_metal_ion_refined 0.047 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5963 Nucleic Acid Atoms Solvent Atoms 1024 Heterogen Atoms 115
Software Software Software Name Purpose SCALA data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling