☰ Navigation Tabs
structure of patulin-detoxifying enzyme Y155F/V187K with NADPH and substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 22-23% PEG Smear Broad, 0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.11 41.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.456 α = 90 b = 64.602 β = 106.83 c = 88.457 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 CMOS BRUKER PHOTON 100 2021-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
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 2.1 35.43 99.4 0.1711 5.36 3.99 53524
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 2.1 2.13 0.4502
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 7XWI 2.1 35.43 49636 2744 97.89 0.202 0.1982 0.2055 0.2706 0.275 RANDOM 23.873
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] 2.11 0.09 -1.42 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.118 r_dihedral_angle_3_deg 17.175 r_dihedral_angle_4_deg 13.915 r_dihedral_angle_1_deg 7.293 r_angle_refined_deg 1.651 r_angle_other_deg 1.298 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.118 r_dihedral_angle_3_deg 17.175 r_dihedral_angle_4_deg 13.915 r_dihedral_angle_1_deg 7.293 r_angle_refined_deg 1.651 r_angle_other_deg 1.298 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6887 Nucleic Acid Atoms Solvent Atoms 602 Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction SAINT data reduction PHENIX phasing