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Crystal structure of Ser67Cys/Pro121Cys Amadoriase I mutant from Aspergillus Fumigatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M sodium citrate pH 5.6
14% PEG4K
15 % isopropanol
Crystal Properties Matthews coefficient Solvent content 2.49 50.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.157 α = 90 b = 83.081 β = 90 c = 175.795 γ = 90
Symmetry Space Group P 21 21 21
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 PSI PILATUS 6M 2017-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 2.1529 47.886 99.9 0.094 15.95 6.8 56549
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 2.1529 2.27 99.7 0.311 6.3 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4wct 2.153 47.886 1.34 56474 2866 99.93 0.1413 0.1392 0.1398 0.1807 0.1807
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 f_dihedral_angle_d 15.129 f_angle_d 1.173 f_chiral_restr 0.077 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6900 Nucleic Acid Atoms Solvent Atoms 923 Heterogen Atoms 178
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing