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Crystal structure of trypsin complexed with 2-(1H-indol-3-yl)ethanamine
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 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.323 α = 90 b = 58.139 β = 90 c = 66.726 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 IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 1.72 50 96.4 0.035 0.035 40.6 6.4 22247 22247 -3 13.4
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 1.72 1.78 90.8 0.077 0.077 18.5 6 2056
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 3A7T 1.72 19.85 21090 21090 1113 99.8 0.15561 0.15561 0.15479 0.1674 0.17141 0.1704 RANDOM 9.571
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] 0.24 -0.14 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.157 r_dihedral_angle_4_deg 19.221 r_dihedral_angle_3_deg 11.114 r_dihedral_angle_1_deg 6.054 r_scangle_it 1.807 r_scbond_it 1.128 r_angle_refined_deg 1.071 r_angle_other_deg 0.789 r_mcangle_it 0.745 r_mcbond_it 0.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.157 r_dihedral_angle_4_deg 19.221 r_dihedral_angle_3_deg 11.114 r_dihedral_angle_1_deg 6.054 r_scangle_it 1.807 r_scbond_it 1.128 r_angle_refined_deg 1.071 r_angle_other_deg 0.789 r_mcangle_it 0.745 r_mcbond_it 0.504 r_symmetry_vdw_other 0.243 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.226 r_nbd_other 0.186 r_nbtor_refined 0.171 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.113 r_nbtor_other 0.083 r_mcbond_other 0.08 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 25
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling