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Crystal Structure of Trypsin complexed with (E)-2-(4-carbamimidoylbenzylideneaminooxy)-2-methylpropanoic acid (soaking 40seconds)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1M Tris-HCl, 30% PEG 3350, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.101 α = 90 b = 56.818 β = 90 c = 66.14 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 IMAGE PLATE RIGAKU RAXIS VII M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 50 98.7 0.081 0.081 15.4 5.5 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.81 98.9 0.289 0.289 3.6 3.8
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 3A7T 1.75 19.65 19644 1044 98.92 0.16514 0.16372 0.1658 0.19301 0.1655 RANDOM 18.297
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] 0.16 -0.24 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.37 r_dihedral_angle_4_deg 17.572 r_dihedral_angle_3_deg 13.352 r_dihedral_angle_1_deg 6.179 r_scangle_it 3.061 r_scbond_it 1.961 r_angle_refined_deg 1.274 r_mcangle_it 1.274 r_mcbond_it 0.742 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.37 r_dihedral_angle_4_deg 17.572 r_dihedral_angle_3_deg 13.352 r_dihedral_angle_1_deg 6.179 r_scangle_it 3.061 r_scbond_it 1.961 r_angle_refined_deg 1.274 r_mcangle_it 1.274 r_mcbond_it 0.742 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.293 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.172 r_metal_ion_refined 0.154 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other 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 271 Heterogen Atoms 19
Software Software Software Name Purpose LAFIRE model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling LAFIRE phasing