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Pyrrolidine fragment 10d bound to endothiapepsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y5L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.1 M sodium acetate pH 4.5, 0.1 M ammonium acetate, 24 - 30 % PEG4000
Crystal Properties Matthews coefficient Solvent content 1.9 35.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.34 α = 90 b = 72.82 β = 109.23 c = 52.76 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 EIGER X 16M 2021-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.15 42.81 94.9 0.044 0.99 21.39 6.16 108821 13.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.25 0.97
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.15 42.81 1.39 108821 5441 94.96 0.1318 0.1309 0.1309 0.1479 0.1479 16.16
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 10.8759 f_angle_d 0.9767 f_chiral_restr 0.0827 f_bond_d 0.0067 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2378 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing