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Engineered Fructosyl Peptide Oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T1E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1 M MES monohydrate pH 6.5, 12% PEG 20 K
Crystal Properties Matthews coefficient Solvent content 2.81 56.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.033 α = 90 b = 90.033 β = 90 c = 131.435 γ = 90
Symmetry Space Group P 42 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 PSI PILATUS 6M 2019-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.35 45.8 100 0.071 0.073 0.014 1 28.8 20 118634
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.42 0.407 0.415 0.083 0.986 9.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5T1E 1.38 45.77 105505 5594 99.99 0.1498 0.1488 0.1691 0.1858 RANDOM 15.52
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] 0.07 0.07 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.214 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 11.687 r_dihedral_angle_1_deg 7.004 r_angle_refined_deg 2.082 r_angle_other_deg 1.536 r_chiral_restr 0.117 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.214 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 11.687 r_dihedral_angle_1_deg 7.004 r_angle_refined_deg 2.082 r_angle_other_deg 1.536 r_chiral_restr 0.117 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3336 Nucleic Acid Atoms Solvent Atoms 673 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing