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TMAO-grown orthorhombic trypsin (bovine)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TPO PDB entry 1TPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 40 mg/mL protein in 50 mM benzamidine, 2 M TMAO, 0.2 M AmSO4, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.934 α = 90 b = 58.576 β = 90 c = 67.941 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 298 CCD OXFORD ONYX CCD 2011-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 44.4 99.9 0.067 16.1 5.3 24788 24788
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 1.7 1.79 100 0.437 0.437 1.5 3.2
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 (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 PDB entry 1TPO 1.7 20.57 24788 23435 1254 99.71 0.15837 0.1568 0.1574 0.1875 0.188 RANDOM 15.104
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] 0.28 -0.21 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.651 r_dihedral_angle_4_deg 19.559 r_dihedral_angle_3_deg 12.634 r_dihedral_angle_1_deg 6.052 r_scangle_it 4.254 r_scbond_it 2.598 r_mcangle_it 1.66 r_angle_refined_deg 1.449 r_mcbond_it 0.891 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.651 r_dihedral_angle_4_deg 19.559 r_dihedral_angle_3_deg 12.634 r_dihedral_angle_1_deg 6.052 r_scangle_it 4.254 r_scbond_it 2.598 r_mcangle_it 1.66 r_angle_refined_deg 1.449 r_mcbond_it 0.891 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 160 Heterogen Atoms 30
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data collection CrysalisPro data reduction