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structure of patulin-detoxifying enzyme Y155F/V187K with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XWH
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 2.1 41.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.338 α = 90 b = 64.902 β = 107.74 c = 89.279 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 1.98 36.17 99.9 0.1456 7.73 5.62 65000
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 1.98 2.01 0.4224
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 7XWH 1.98 36.17 61232 3243 99.22 0.2032 0.1999 0.2074 0.2678 0.2718 RANDOM 20.658
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] 1.53 0.93 -1.22 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.086 r_dihedral_angle_3_deg 15.812 r_dihedral_angle_4_deg 14.367 r_dihedral_angle_1_deg 6.914 r_angle_refined_deg 1.51 r_angle_other_deg 1.289 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.086 r_dihedral_angle_3_deg 15.812 r_dihedral_angle_4_deg 14.367 r_dihedral_angle_1_deg 6.914 r_angle_refined_deg 1.51 r_angle_other_deg 1.289 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 953 Heterogen Atoms 192
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction PHENIX phasing