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Crystal Structure of Trypsin complexed with (E)-4-((tetrahydro-2H-pyran-2-yloxyimino)methyl)benzimidamide (soaking 4hours)
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 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.447 α = 90 b = 58.542 β = 90 c = 66.562 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 99.9 0.059 0.059 25.6 6.8 -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 99.3 0.148 0.148 8.1 4.9
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 19.94 20739 1085 99.15 0.14313 0.1418 0.1472 0.16827 0.1459 RANDOM 11.823
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] 0.12 -0.06 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.627 r_dihedral_angle_4_deg 16.024 r_dihedral_angle_3_deg 11.301 r_dihedral_angle_1_deg 6.193 r_scangle_it 2.676 r_scbond_it 1.684 r_angle_refined_deg 1.176 r_mcangle_it 1.042 r_mcbond_it 0.601 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.627 r_dihedral_angle_4_deg 16.024 r_dihedral_angle_3_deg 11.301 r_dihedral_angle_1_deg 6.193 r_scangle_it 2.676 r_scbond_it 1.684 r_angle_refined_deg 1.176 r_mcangle_it 1.042 r_mcbond_it 0.601 r_nbtor_refined 0.301 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.143 r_metal_ion_refined 0.138 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 395 Heterogen Atoms 30
Software Software Software Name Purpose LAFIRE model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling LAFIRE phasing