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Endothiapepsin in complex with compound TL00150 at room-temperature (temperature ramping down structure 10)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RSV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 0.1 M ammonium acetate, 0.1 M sodium acetate pH 4.6, and 26 - 30% (v/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.97 37.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.86 α = 90 b = 74.009 β = 109.594 c = 53.458 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 273 PIXEL DECTRIS EIGER2 X 16M 2021-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 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 1.79 35.26 99.85 0.09 0.99 13.57 6.83 31678 25.53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.86 99.33 0.7 0.83 2.37 6.41
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 6RSV 1.79 35.26 1.37 31666 1569 99.86 0.1771 0.1757 0.176 0.2063 0.2057 28.63
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 7.8325 f_angle_d 0.6869 f_chiral_restr 0.0511 f_plane_restr 0.0039 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2379 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 48
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement