☰ Navigation Tabs
The crystal structure of VyPAL2-I244V, a more efficient mutant 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 293.15 0.1 M Bis-Tris pH 5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.27 α = 90 b = 78.98 β = 90 c = 92.12 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 2020-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.593 46.06 99.26 0.08307 0.08643 0.02365 0.999 16.5 13.4 74533 29.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.593 1.65 92.83 0.8825 0.449 0.83 12.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6IDV 1.593 46.06 74372 3721 99.26 0.1631 0.1641 0.1927 0.192 RANDOM 37.91
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] 6.9977 -4.1657 -2.832
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.9 t_omega_torsion 3.7 t_angle_deg 0.95 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4215 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 172
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction XDS data scaling MOLREP phasing