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Turning an asparaginyl endopeptidase into a peptide ligase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6L4V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% v/v PEG 500* MME, 10 % w/v PEG 20000,
0.1M Sodium formate, 0.1M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Potassium sodium tartrate tetrahydrate, 0.1M Sodium oxamate,
0.1M Sodium HEPES, MOPS (acid)
Crystal Properties Matthews coefficient Solvent content 2.15 42.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.55 α = 90 b = 79.74 β = 90 c = 135.02 γ = 90
Symmetry Space Group P 2 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 PILATUS 2M-F 2019-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000030 SLS X06DA
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 2 42.31 99.96 0.093 1 22.66 13 60392 32.12
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 2 2.07 1.076 0.784
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6L4V 2 42.31 1.32 60392 3019 96.2 0.1938 0.1932 0.1935 0.2052 0.2049 37.4
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.8599 f_angle_d 1.3428 f_chiral_restr 0.0951 f_bond_d 0.0129 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3207 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling MOLREP phasing