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Crystal structure of Thomasclavelia ramosa IgA peptidase (IgAse) active site mutant (E330-N876)
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 8 293 PEG3350, sodium fluoride
Crystal Properties Matthews coefficient Solvent content 2.12 42.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.15 α = 90 b = 87.83 β = 96.11 c = 67.47 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 PILATUS3 X 6M KB mirrors (VFM and HFM in Kirkpatrick-Baez configuration) 2023-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.75 45.9 99.1 0.077 0.083 0.99 13.3 6.4 53460
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 1.75 1.86 96 1.563 0.458 1.23 4.9
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 1.75 45.89 53460 701 99.2 0.1784 0.1779 0.1706 0.2133 0.1991 RANDOM 36.48
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] -0.7847 0.03 -2.1139 2.8987
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.86 t_other_torsion 2.55 t_angle_deg 0.88 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_utility_distance
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.86 t_other_torsion 2.55 t_angle_deg 0.88 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4409 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 50
Software Software Software Name Purpose BUSTER refinement SHELXE model building XDS data reduction XSCALE data scaling PHASER phasing