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Crystal structure of Bovine Pancreatic Trypsin in complex with Benzamidine at Room Temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 100mM Tris-HCl, 30 %(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.58 α = 90 b = 58.31 β = 90 c = 67.35 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 293 PIXEL DECTRIS EIGER X 4M 2021-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1
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 1.77 50 98.3 0.197 0.99 10.03 5.15 21236 16.7
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 1.77 1.88 98.4 1.494 0.499 2.36 5.11
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 1s0r 1.77 44.08 20176 1025 98.33 0.13788 0.13461 0.1495 0.19901 0.203 RANDOM 18.702
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] -0.43 3.16 -2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.448 r_dihedral_angle_4_deg 22.196 r_dihedral_angle_3_deg 14.632 r_dihedral_angle_1_deg 7.248 r_rigid_bond_restr 6.751 r_scangle_other 5.293 r_long_range_B_refined 4.977 r_long_range_B_other 4.959 r_scbond_it 4.341 r_scbond_other 4.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.448 r_dihedral_angle_4_deg 22.196 r_dihedral_angle_3_deg 14.632 r_dihedral_angle_1_deg 7.248 r_rigid_bond_restr 6.751 r_scangle_other 5.293 r_long_range_B_refined 4.977 r_long_range_B_other 4.959 r_scbond_it 4.341 r_scbond_other 4.339 r_mcangle_it 3.593 r_mcangle_other 3.592 r_mcbond_other 2.896 r_mcbond_it 2.895 r_angle_refined_deg 1.772 r_angle_other_deg 1.468 r_chiral_restr 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing