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Crystal structure of trypsin complexed with (3-methoxyphenyl)methanamine
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 45.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.361 α = 90 b = 57.974 β = 90 c = 66.84 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 1.71 50 96.4 0.057 0.057 24.8 6.1 22624 22624 -3 17.8
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 1.71 1.77 90.3 0.194 0.194 6.2 5.2 2079
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 1.71 19.83 21295 21295 1111 99.11 0.19398 0.19398 0.19246 0.2032 0.2227 0.1991 RANDOM 12.316
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] -0.45 0.8 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.829 r_dihedral_angle_4_deg 18.662 r_dihedral_angle_3_deg 12.213 r_dihedral_angle_1_deg 6.3 r_scangle_it 1.875 r_scbond_it 1.25 r_angle_refined_deg 1.118 r_symmetry_vdw_refined 0.864 r_angle_other_deg 0.807 r_mcangle_it 0.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.829 r_dihedral_angle_4_deg 18.662 r_dihedral_angle_3_deg 12.213 r_dihedral_angle_1_deg 6.3 r_scangle_it 1.875 r_scbond_it 1.25 r_angle_refined_deg 1.118 r_symmetry_vdw_refined 0.864 r_angle_other_deg 0.807 r_mcangle_it 0.765 r_mcbond_it 0.487 r_symmetry_vdw_other 0.321 r_nbd_refined 0.244 r_nbd_other 0.189 r_symmetry_hbond_refined 0.18 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.103 r_mcbond_other 0.092 r_nbtor_other 0.084 r_chiral_restr 0.072 r_bond_refined_d 0.007 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 287 Heterogen Atoms 27
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling