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Crystal Structure of Trypsin complexed with (E)-2-(4-carbamimidoylbenzylideneaminooxy)acetic acid (under aniline-free condition)
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 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.06 α = 90 b = 56.888 β = 90 c = 66.22 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 99.6 0.045 0.045 25.8 5.6 -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 98.5 0.171 0.171 6.2 4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3A7T 1.75 19.65 19955 1060 99.55 0.1547 0.15317 0.18287 0.2523 RANDOM 15.525
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] 0.13 0.04 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.814 r_dihedral_angle_4_deg 20.416 r_dihedral_angle_3_deg 10.991 r_dihedral_angle_1_deg 6.087 r_scangle_it 3.157 r_scbond_it 1.995 r_angle_refined_deg 1.276 r_mcangle_it 1.221 r_mcbond_it 0.702 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.814 r_dihedral_angle_4_deg 20.416 r_dihedral_angle_3_deg 10.991 r_dihedral_angle_1_deg 6.087 r_scangle_it 3.157 r_scbond_it 1.995 r_angle_refined_deg 1.276 r_mcangle_it 1.221 r_mcbond_it 0.702 r_nbtor_refined 0.296 r_nbd_refined 0.186 r_symmetry_hbond_refined 0.167 r_symmetry_vdw_refined 0.15 r_metal_ion_refined 0.133 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.091 r_bond_refined_d 0.011 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 247 Heterogen Atoms 47
Software Software Software Name Purpose LAFIRE model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling LAFIRE phasing