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Crystal structure of the unliganded PNGaseABif E236Q mutant
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 291 peg 8000
AmSo4
Crystal Properties Matthews coefficient Solvent content 2.18 43.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.417 α = 90 b = 77.674 β = 109.5 c = 80.212 γ = 90
Symmetry Space Group C 1 2 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 6M 2025-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 75.61 88.9 0.1 0.996 7.7 3.8 40665
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 1.018 0.534
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 1.8 75.61 38566 2074 88.73 0.20286 0.20079 0.2082 0.24013 0.2444 RANDOM 31.15
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] -1.46 -1 2.2 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.749 r_dihedral_angle_2_deg 10.842 r_long_range_B_other 9.22 r_long_range_B_refined 9.214 r_dihedral_angle_1_deg 7.409 r_scangle_other 6.201 r_mcangle_it 5.555 r_mcangle_other 5.554 r_scbond_it 3.868 r_scbond_other 3.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.749 r_dihedral_angle_2_deg 10.842 r_long_range_B_other 9.22 r_long_range_B_refined 9.214 r_dihedral_angle_1_deg 7.409 r_scangle_other 6.201 r_mcangle_it 5.555 r_mcangle_other 5.554 r_scbond_it 3.868 r_scbond_other 3.867 r_mcbond_it 3.483 r_mcbond_other 3.481 r_angle_refined_deg 1.66 r_angle_other_deg 0.582 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 4056 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing