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Crystal structure of trypsin-guanidine complex at 2.05 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 291 0.1-0.4 M Li2SO4, 16% PEG-3350 and 0.1 M HEPES at pH of 7.8
Crystal Properties Matthews coefficient Solvent content 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.394 α = 90 b = 58.042 β = 90 c = 66.189 γ = 90
Symmetry Space Group P 21 21 21
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 Bruker PHOTON II 2022-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 18.57 99.9 0.197 0.98 12.8 6.9 14694
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.703 0.82 3.6
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 1CE5 2 18.58 13859 793 99.8 0.17126 0.16834 0.1784 0.22517 0.2325 RANDOM 9.323
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] -0.03 0.21 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.193 r_dihedral_angle_4_deg 18.126 r_dihedral_angle_3_deg 15.586 r_dihedral_angle_1_deg 7.884 r_long_range_B_refined 3.986 r_long_range_B_other 3.734 r_scangle_other 1.905 r_angle_refined_deg 1.661 r_angle_other_deg 1.414 r_scbond_it 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.193 r_dihedral_angle_4_deg 18.126 r_dihedral_angle_3_deg 15.586 r_dihedral_angle_1_deg 7.884 r_long_range_B_refined 3.986 r_long_range_B_other 3.734 r_scangle_other 1.905 r_angle_refined_deg 1.661 r_angle_other_deg 1.414 r_scbond_it 1.27 r_scbond_other 1.246 r_mcangle_it 1.17 r_mcangle_other 1.17 r_mcbond_it 0.715 r_mcbond_other 0.715 r_chiral_restr 0.067 r_bond_refined_d 0.01 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 1629 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction Aimless data scaling MOLREP phasing