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Copper Complex of Peanut USP-type BURP Domain Peptide Cyclase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SY2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.4 295.2 2.7 M sodium formate, 0.1 M Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.12 60.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.407 α = 90 b = 105.407 β = 90 c = 223.838 γ = 120
Symmetry Space Group P 61 2 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 EIGER X 16M 2022-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.3777 APS 23-ID-B
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 3.2 70.74 99.7 0.118 0.129 0.051 0.996 8.8 6.3 12803
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 3.2 3.42 99.9 1.314 1.425 0.543 0.628 6.7
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 3.2 70.74 12133 613 99.53 0.22972 0.22777 0.2314 0.26887 0.2674 RANDOM 135.162
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] 0.19 0.09 0.19 -0.62
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 25.512 r_long_range_B_refined 25.511 r_mcangle_other 17.761 r_mcangle_it 17.757 r_scangle_other 17.721 r_dihedral_angle_3_deg 15.703 r_scbond_it 12.074 r_scbond_other 12.056 r_mcbond_it 11.799 r_mcbond_other 11.798
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 25.512 r_long_range_B_refined 25.511 r_mcangle_other 17.761 r_mcangle_it 17.757 r_scangle_other 17.721 r_dihedral_angle_3_deg 15.703 r_scbond_it 12.074 r_scbond_other 12.056 r_mcbond_it 11.799 r_mcbond_other 11.798 r_dihedral_angle_2_deg 8.868 r_dihedral_angle_1_deg 8.023 r_angle_refined_deg 1.661 r_angle_other_deg 0.589 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 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 3237 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing Coot model building xia2 data reduction DIALS data reduction