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Crystal structure of trypsin in-complex with E-64
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SY3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 0.1 M HEPES (pH = 7.8), 16% PEG 3350, and 0.1-0.4 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 1.96 37.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.418 α = 90 b = 54.418 β = 90 c = 107.058 γ = 120
Symmetry Space Group P 31 2 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 CMOS BRUKER PHOTON 100 2021-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54
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 2.3 17.82 99.8 0.103 0.108 0.99 25 10.6 8610
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 2.3 2.3 100 0.313 0.331 0.96 8.7 9.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6SY3 2.3 17.82 8218 362 99.71 0.16291 0.15943 0.1723 0.24784 0.2525 RANDOM 10.809
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] 0.02 0.01 0.02 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.457 r_dihedral_angle_4_deg 24.138 r_dihedral_angle_3_deg 14.99 r_dihedral_angle_1_deg 7.915 r_long_range_B_refined 3.06 r_long_range_B_other 3.059 r_angle_refined_deg 1.485 r_scangle_other 1.38 r_angle_other_deg 1.272 r_mcangle_it 1.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.457 r_dihedral_angle_4_deg 24.138 r_dihedral_angle_3_deg 14.99 r_dihedral_angle_1_deg 7.915 r_long_range_B_refined 3.06 r_long_range_B_other 3.059 r_angle_refined_deg 1.485 r_scangle_other 1.38 r_angle_other_deg 1.272 r_mcangle_it 1.031 r_mcangle_other 1.031 r_scbond_it 0.825 r_scbond_other 0.825 r_mcbond_it 0.603 r_mcbond_other 0.603 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 1628 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction Aimless data scaling MOLREP phasing