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Engineered Fructosyl Peptide Oxidase - X02B mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y4J 6Y4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG 20000 16-26%, MES 0.1M pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.64 53.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.112 α = 90 b = 88.493 β = 90 c = 90.938 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 DECTRIS EIGER2 XE 16M 2022-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.475 63.421 96 0.067 0.07 16.7 12.7 82805
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.475 1.501 100 0.4 11.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6Y4J 1.475 63.421 80871 4009 93.716 0.191 0.1893 0.1923 0.2149 0.2175 26.915
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] 1.441 -0.256 -1.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.566 r_dihedral_angle_2_deg 16.113 r_dihedral_angle_3_deg 13.669 r_lrange_it 7.985 r_lrange_other 7.889 r_dihedral_angle_1_deg 7.263 r_scangle_it 5.569 r_scangle_other 5.568 r_mcangle_other 3.878 r_mcangle_it 3.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.566 r_dihedral_angle_2_deg 16.113 r_dihedral_angle_3_deg 13.669 r_lrange_it 7.985 r_lrange_other 7.889 r_dihedral_angle_1_deg 7.263 r_scangle_it 5.569 r_scangle_other 5.568 r_mcangle_other 3.878 r_mcangle_it 3.875 r_scbond_it 3.801 r_scbond_other 3.8 r_mcbond_it 2.69 r_mcbond_other 2.689 r_angle_refined_deg 1.697 r_angle_other_deg 0.582 r_symmetry_nbd_refined 0.449 r_nbd_other 0.289 r_symmetry_xyhbond_nbd_refined 0.257 r_nbd_refined 0.225 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_other 0.089 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.079 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3342 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement autoPROC data processing Aimless data scaling Coot model building MOLREP phasing Coot model building XDS data reduction