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Bovine trypsin variant X(tripleGlu217Phe227) in complex with small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V2K PDB ENTRY 1V2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 30% PEG8000, 0.3M AMMONIUM SULPHATE, 0.1M IMIDAZOLE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.71 54.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.069 α = 89.62 b = 98.569 β = 88.85 c = 120.781 γ = 103.99
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.22 120.78 89.25 0.13 5.1 56715 -3.7 56
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1V2K 3.22 120.78 56715 56715 568 89.25 0.2072 0.2072 0.2054 0.2609 0.2318 RANDOM 32.138
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] -0.11 10.56 -5.51 -29.61 -5.42 29.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.985 r_dihedral_angle_3_deg 16.26 r_dihedral_angle_4_deg 11.99 r_dihedral_angle_1_deg 6.523 r_angle_refined_deg 1.603 r_angle_other_deg 1.028 r_chiral_restr 0.088 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.985 r_dihedral_angle_3_deg 16.26 r_dihedral_angle_4_deg 11.99 r_dihedral_angle_1_deg 6.523 r_angle_refined_deg 1.603 r_angle_other_deg 1.028 r_chiral_restr 0.088 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26224 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 163
Software Software Software Name Purpose DENZO data reduction AMoRE phasing REFMAC refinement SCALEPACK data scaling