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Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SFI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 291 sodium acetate trihydrate (0,1 M) at pH 4.6, amonium sulfate (0.3 M) and polyethylene glycol 8000 (30%)
Crystal Properties Matthews coefficient Solvent content 2.66 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.738 α = 90 b = 62.993 β = 90 c = 68.961 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 PIXEL DECTRIS PILATUS 6M 2013-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0 PETRA III, EMBL c/o DESY P13 (MX1)
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 1 46.51 98.09 0.042 30.57 13 142495
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.036 94.55 0.373 6.05 12.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1SFI 1 46.51 135158 7151 97.96 0.09573 0.09527 0.0928 0.10434 0.1025 RANDOM 10.955
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] 0.16 0.04 -0.2
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 48.401 r_dihedral_angle_2_deg 39.519 r_dihedral_angle_4_deg 15.788 r_sphericity_bonded 14.393 r_rigid_bond_restr 10.977 r_dihedral_angle_3_deg 9.72 r_long_range_B_refined 7.729 r_dihedral_angle_1_deg 7.127 r_long_range_B_other 5.687 r_scangle_other 2.501
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 48.401 r_dihedral_angle_2_deg 39.519 r_dihedral_angle_4_deg 15.788 r_sphericity_bonded 14.393 r_rigid_bond_restr 10.977 r_dihedral_angle_3_deg 9.72 r_long_range_B_refined 7.729 r_dihedral_angle_1_deg 7.127 r_long_range_B_other 5.687 r_scangle_other 2.501 r_scbond_it 2.257 r_scbond_other 2.257 r_angle_other_deg 2.189 r_angle_refined_deg 2.015 r_mcangle_other 1.32 r_mcangle_it 1.318 r_mcbond_it 1.051 r_mcbond_other 1.035 r_chiral_restr 0.202 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_gen_planes_other 0.01 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1732 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing