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The crystal structure of VyPAL2-C214A, a dead mutant of VyPAL2 peptide asparaginyl ligase in form II
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 0.2 M Potassium formate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 45.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.495 α = 90 b = 78.546 β = 90 c = 92.67 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 2021-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00001 SLS X06SA
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 1.8 46.33 99.09 0.09147 0.09946 0.03844 0.997 12.65 6.7 51971 27.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.864 98.35 1.008 1.1 0.4336 0.698 2.12 6.2
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 (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 6IDV 1.8 46.33 51968 2618 99.1 0.1688 0.1636 0.1639 0.1944 0.1899 RANDOM 33.24
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] -1.0547 -0.5928 1.6475
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.31 t_omega_torsion 3.59 t_angle_deg 0.96 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 4270 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 124
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction XDS data scaling MOLREP phasing