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Ancestral Prenylcysteine Oxidase 1 (PCYOX1)
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, HANGING DROP 6.5 293 2.0 M Ammonium Sulfate, 0.1 M HEPES, 5% Isopropanol, pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.89 68.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.659 α = 90 b = 172.659 β = 90 c = 172.659 γ = 90
Symmetry Space Group P 41 3 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 DECTRIS PILATUS3 6M 2024-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.969 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 3.1 172.77 100 0.18 0.19 0.03 1 15.3 57.6 16624
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 3.1 3.31 100 0.34 1.56 26.7
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 3.1 122.39 14894 1646 99.79 0.23015 0.22528 0.2438 0.27546 0.288 RANDOM 150.297
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]
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 27.407 r_long_range_B_other 27.407 r_scangle_other 18.516 r_dihedral_angle_3_deg 17.094 r_mcangle_it 15.57 r_mcangle_other 15.567 r_scbond_it 12.251 r_scbond_other 12.188 r_dihedral_angle_2_deg 11.764 r_mcbond_it 10.432
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 27.407 r_long_range_B_other 27.407 r_scangle_other 18.516 r_dihedral_angle_3_deg 17.094 r_mcangle_it 15.57 r_mcangle_other 15.567 r_scbond_it 12.251 r_scbond_other 12.188 r_dihedral_angle_2_deg 11.764 r_mcbond_it 10.432 r_mcbond_other 10.42 r_dihedral_angle_1_deg 7.809 r_angle_refined_deg 1.993 r_angle_other_deg 0.631 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 3654 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing