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Patulin Synthase from Penicillium expansum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Calcium chloride, PEG6000 and sodium acetate pH 5
Crystal Properties Matthews coefficient Solvent content 2.87 57.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.841 α = 90 b = 144.163 β = 91.53 c = 155.24 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 PIXEL DECTRIS PILATUS 2M 2022-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
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 2.4 48.74 100 0.155 0.168 0.064 0.978 9.5 6.9 179872
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 2.4 2.44 100 1.113 1.211 0.47 0.72 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.4 48.74 170431 9411 99.98 0.18429 0.18222 0.1878 0.22244 0.2258 RANDOM 37.378
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] 2.32 -1.6 -0.22 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.423 r_dihedral_angle_4_deg 18.581 r_dihedral_angle_3_deg 14.676 r_long_range_B_refined 10.661 r_long_range_B_other 10.661 r_scangle_other 10.179 r_scbond_it 8.092 r_scbond_other 8.092 r_dihedral_angle_1_deg 7.379 r_mcangle_it 7.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.423 r_dihedral_angle_4_deg 18.581 r_dihedral_angle_3_deg 14.676 r_long_range_B_refined 10.661 r_long_range_B_other 10.661 r_scangle_other 10.179 r_scbond_it 8.092 r_scbond_other 8.092 r_dihedral_angle_1_deg 7.379 r_mcangle_it 7.168 r_mcangle_other 7.168 r_mcbond_it 5.929 r_mcbond_other 5.928 r_angle_refined_deg 1.528 r_angle_other_deg 1.263 r_chiral_restr 0.066 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 27028 Nucleic Acid Atoms Solvent Atoms 979 Heterogen Atoms 1059
Software Software Software Name Purpose Aimless data scaling REFMAC refinement XDS data reduction PHASER phasing