☰ Navigation Tabs
Crystal Structure of the complex formed between trypsin and a designed synthetic highly potent inhibitor in the presence of benzamidine at 0.97 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JRT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290 5mM MES, 1mM CaCl2, 2.5mM benzamidine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.1 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.55 α = 90 b = 68.55 β = 90 c = 73.33 γ = 120
Symmetry Space Group P 32 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 IMAGE PLATE MARRESEARCH Mirror 2000-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.91 EMBL/DESY, HAMBURG BW7B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 0.97 20 99.6 0.065 18.2 225251 116664 7.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.97 1 95.5 0.401 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1JRT 0.97 20 116664 114997 1167 99.6 0.13773 0.13773 0.13355 0.1426 0.15683 0.1635 RANDOM 9.672
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] -0.15 -0.08 -0.15 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.973 r_dihedral_angle_4_deg 18.526 r_dihedral_angle_3_deg 13.236 r_dihedral_angle_1_deg 6.727 r_sphericity_free 5.517 r_scangle_it 3.27 r_scbond_it 3.038 r_angle_other_deg 2.908 r_sphericity_bonded 2.546 r_rigid_bond_restr 1.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.973 r_dihedral_angle_4_deg 18.526 r_dihedral_angle_3_deg 13.236 r_dihedral_angle_1_deg 6.727 r_sphericity_free 5.517 r_scangle_it 3.27 r_scbond_it 3.038 r_angle_other_deg 2.908 r_sphericity_bonded 2.546 r_rigid_bond_restr 1.945 r_mcangle_it 1.794 r_angle_refined_deg 1.66 r_mcbond_it 1.284 r_mcbond_other 0.548 r_symmetry_vdw_other 0.281 r_symmetry_vdw_refined 0.244 r_symmetry_hbond_refined 0.243 r_nbd_refined 0.206 r_nbd_other 0.191 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.104 r_metal_ion_refined 0.097 r_nbtor_other 0.094 r_gen_planes_refined 0.019 r_bond_refined_d 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling AMoRE phasing