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Gamma-glutamyl peptidase 1 from Arabidopsis thaliana (inactive form)
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 4.5 277 sodium acetate, sodium dihydrogen phsophate, di-potassium hydrogen phsophate
Crystal Properties Matthews coefficient Solvent content 2.35 47.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.354 α = 90 b = 75.329 β = 90 c = 102.583 γ = 90
Symmetry Space Group P 21 21 21
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 2023-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.04 46.55 100 0.096 0.04 0.998 13.5 6.7 36242 22.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.1 99.9 0.569 0.232 0.895 3.4 6.9
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 2.04 46.55 34305 1878 99.94 0.17955 0.17655 0.1872 0.23323 0.2376 RANDOM 30.604
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] 0.05 -0.94 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.432 r_dihedral_angle_2_deg 12.867 r_long_range_B_other 9.065 r_long_range_B_refined 9.064 r_scangle_other 8.029 r_dihedral_angle_1_deg 6.656 r_scbond_it 5.601 r_scbond_other 5.6 r_mcangle_it 5.114 r_mcangle_other 5.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.432 r_dihedral_angle_2_deg 12.867 r_long_range_B_other 9.065 r_long_range_B_refined 9.064 r_scangle_other 8.029 r_dihedral_angle_1_deg 6.656 r_scbond_it 5.601 r_scbond_other 5.6 r_mcangle_it 5.114 r_mcangle_other 5.113 r_mcbond_it 3.961 r_mcbond_other 3.896 r_angle_refined_deg 2.554 r_angle_other_deg 0.815 r_chiral_restr 0.118 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 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 3930 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing