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Crystal structure of trypsin complexed with benzamidine
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 45.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.624 α = 90 b = 58.105 β = 90 c = 66.41 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 1.74 50 94.4 0.087 0.087 15.6 5.7 21074 21074 -3 17.3
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 1.74 1.8 90.7 0.21 0.21 6.3 5.5 2000
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 1.74 19.9 19887 19887 1059 99.44 0.16079 0.16079 0.15935 0.1743 0.18752 0.1753 RANDOM 11.713
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] 0.32 -0.82 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.757 r_dihedral_angle_4_deg 19.505 r_dihedral_angle_3_deg 10.648 r_dihedral_angle_1_deg 6.095 r_scangle_it 1.742 r_scbond_it 1.196 r_angle_refined_deg 1.062 r_angle_other_deg 0.791 r_mcangle_it 0.737 r_mcbond_it 0.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.757 r_dihedral_angle_4_deg 19.505 r_dihedral_angle_3_deg 10.648 r_dihedral_angle_1_deg 6.095 r_scangle_it 1.742 r_scbond_it 1.196 r_angle_refined_deg 1.062 r_angle_other_deg 0.791 r_mcangle_it 0.737 r_mcbond_it 0.502 r_symmetry_vdw_other 0.25 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.197 r_nbd_other 0.19 r_symmetry_hbond_refined 0.184 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.11 r_mcbond_other 0.09 r_nbtor_other 0.084 r_chiral_restr 0.064 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 317 Heterogen Atoms 22
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling