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The crystal structure of VyPAL2 peptide asparaginyl ligase in its active enzyme form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293.15 0.2 M lithium sulfate, 0.1 M sodium acetate, pH 4.5, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.47 50.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.57 α = 90 b = 63.88 β = 90 c = 151.88 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 9M 2020-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 0.99999 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 48.88 99.96 0.419 7.51 10.3 28255 27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.382 100 2.141 1.32 10.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6IDV 2.3 48.88 28250 1351 99.96 0.176 0.1748 0.1744 0.2174 0.2162 28.69
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] -1.446 1.373 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.373 r_dihedral_angle_3_deg 13.878 r_dihedral_angle_4_deg 11.758 r_lrange_it 6.579 r_dihedral_angle_1_deg 6.302 r_scangle_it 4.924 r_scbond_it 3.18 r_mcangle_it 2.851 r_mcbond_it 1.794 r_angle_refined_deg 1.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.373 r_dihedral_angle_3_deg 13.878 r_dihedral_angle_4_deg 11.758 r_lrange_it 6.579 r_dihedral_angle_1_deg 6.302 r_scangle_it 4.924 r_scbond_it 3.18 r_mcangle_it 2.851 r_mcbond_it 1.794 r_angle_refined_deg 1.429 r_nbtor_refined 0.317 r_symmetry_nbd_refined 0.216 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.103 r_symmetry_xyhbond_nbd_refined 0.081 r_ncsr_local_group_1 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4327 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XDS data scaling MOLREP phasing