☰ Navigation Tabs
Engineered Fructosyl Peptide Oxidase - X04 mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
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 2.78 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.238 α = 90 b = 90.238 β = 90 c = 131.437 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 2022-04-08 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) 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 1.6 74.393 94.7 0.999 20.5 16.1 62950
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.673 0.458 1.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6Y4J 1.6 45.82 57975 3052 84.57 0.1669 0.16546 0.178 0.19411 0.2059 RANDOM 18.791
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] 1.78 1.78 -3.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.482 r_dihedral_angle_2_deg 8.442 r_long_range_B_refined 7.478 r_long_range_B_other 7.217 r_dihedral_angle_1_deg 6.718 r_scangle_other 4.888 r_scbond_it 3.325 r_scbond_other 3.325 r_mcangle_other 2.7 r_mcangle_it 2.699
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.482 r_dihedral_angle_2_deg 8.442 r_long_range_B_refined 7.478 r_long_range_B_other 7.217 r_dihedral_angle_1_deg 6.718 r_scangle_other 4.888 r_scbond_it 3.325 r_scbond_other 3.325 r_mcangle_other 2.7 r_mcangle_it 2.699 r_mcbond_it 1.823 r_mcbond_other 1.823 r_angle_refined_deg 1.685 r_angle_other_deg 0.592 r_chiral_restr 0.087 r_gen_planes_refined 0.013 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3445 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data processing Aimless data scaling PHASER phasing XDS data reduction