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Crystal structure of Endothiapepsin in complex with fragment EOS102489 from ECBL-96
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 4.6 293 29 % (w/v) PEG 4000, 0.1 M ammonium acetate and 0.1 M sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.43 49.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.32 α = 90 b = 72.99 β = 109.47 c = 52.7 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 PILATUS3 6M 2021-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.05 42.73 94.9 0.073 0.087 0.999 8.38 142872
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.11 89.1 1.508 1.799 0.381
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.05 42.73 140771 2101 94.95 0.17378 0.17359 0.183 0.18658 0.1926 RANDOM 11.548
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] -0.3 -0.38 0.15 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.953 r_dihedral_angle_4_deg 16.83 r_dihedral_angle_3_deg 9.991 r_dihedral_angle_1_deg 6.757 r_long_range_B_refined 3.55 r_long_range_B_other 3.312 r_scangle_other 1.991 r_angle_refined_deg 1.714 r_angle_other_deg 1.621 r_mcangle_other 1.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.953 r_dihedral_angle_4_deg 16.83 r_dihedral_angle_3_deg 9.991 r_dihedral_angle_1_deg 6.757 r_long_range_B_refined 3.55 r_long_range_B_other 3.312 r_scangle_other 1.991 r_angle_refined_deg 1.714 r_angle_other_deg 1.621 r_mcangle_other 1.505 r_mcangle_it 1.504 r_scbond_it 1.298 r_scbond_other 1.298 r_mcbond_it 0.917 r_mcbond_other 0.917 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data scaling XDS data reduction