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Crystal Structure of Trypsin complexed with pre-synthesized (E)-4-((2-nicotinoylhydrazono)methyl)benzimidamide
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 2.27 45.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.521 α = 90 b = 58.424 β = 90 c = 66.555 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 1.78 50 97.8 0.045 0.045 34.3 7.1 -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) 1.78 1.84 92.4 0.065 0.065 23.3 6.5
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 1.78 19.93 19450 1043 99.94 0.14564 0.14367 0.1467 0.18444 0.1387 RANDOM 10.682
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 -0.14 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.817 r_dihedral_angle_4_deg 16.291 r_dihedral_angle_3_deg 12.087 r_dihedral_angle_1_deg 6.176 r_scangle_it 2.716 r_scbond_it 1.759 r_angle_refined_deg 1.181 r_mcangle_it 1.104 r_mcbond_it 0.635 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.817 r_dihedral_angle_4_deg 16.291 r_dihedral_angle_3_deg 12.087 r_dihedral_angle_1_deg 6.176 r_scangle_it 2.716 r_scbond_it 1.759 r_angle_refined_deg 1.181 r_mcangle_it 1.104 r_mcbond_it 0.635 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.246 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.148 r_metal_ion_refined 0.127 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.081 r_bond_refined_d 0.01 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 388 Heterogen Atoms 27
Software Software Software Name Purpose LAFIRE model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling LAFIRE phasing