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Crystal structure of Endothiapepsin in complex with fragment EOS103253 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 2.42 49.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.19 α = 90 b = 72.97 β = 109.27 c = 52.49 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 1.12 42.66 97.6 0.073 0.088 0.999 8.61 121321
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 1.12 1.18 94.4 1.309 1.586 0.356
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 1.12 42.66 119218 2100 97.73 0.17269 0.17221 0.1799 0.20018 0.1962 RANDOM 12.258
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] -0.49 -0.31 0.19 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.708 r_dihedral_angle_4_deg 19.407 r_dihedral_angle_3_deg 9.729 r_dihedral_angle_1_deg 6.596 r_long_range_B_refined 3.215 r_long_range_B_other 3.009 r_scangle_other 1.919 r_angle_refined_deg 1.624 r_angle_other_deg 1.594 r_mcangle_other 1.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.708 r_dihedral_angle_4_deg 19.407 r_dihedral_angle_3_deg 9.729 r_dihedral_angle_1_deg 6.596 r_long_range_B_refined 3.215 r_long_range_B_other 3.009 r_scangle_other 1.919 r_angle_refined_deg 1.624 r_angle_other_deg 1.594 r_mcangle_other 1.387 r_mcangle_it 1.386 r_scbond_it 1.209 r_scbond_other 1.209 r_mcbond_other 0.824 r_mcbond_it 0.818 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 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 270 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data scaling XDS data reduction