4U2W

Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.6291sodium acetate trihydrate (0,1 M) at pH 4.6, amonium sulfate (0.3 M) and polyethylene glycol 8000 (30%)
Crystal Properties
Matthews coefficientSolvent content
2.6653.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.738α = 90
b = 62.993β = 90
c = 68.961γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.0PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1146.5198.090.04230.5713142495
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
111.03694.550.3736.0512.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1SFI146.51135158715197.960.095730.095270.10434RANDOM10.955
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]
0.160.04-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free48.401
r_dihedral_angle_2_deg39.519
r_dihedral_angle_4_deg15.788
r_sphericity_bonded14.393
r_rigid_bond_restr10.977
r_dihedral_angle_3_deg9.72
r_long_range_B_refined7.729
r_dihedral_angle_1_deg7.127
r_long_range_B_other5.687
r_scangle_other2.501
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free48.401
r_dihedral_angle_2_deg39.519
r_dihedral_angle_4_deg15.788
r_sphericity_bonded14.393
r_rigid_bond_restr10.977
r_dihedral_angle_3_deg9.72
r_long_range_B_refined7.729
r_dihedral_angle_1_deg7.127
r_long_range_B_other5.687
r_scangle_other2.501
r_scbond_it2.257
r_scbond_other2.257
r_angle_other_deg2.189
r_angle_refined_deg2.015
r_mcangle_other1.32
r_mcangle_it1.318
r_mcbond_it1.051
r_mcbond_other1.035
r_chiral_restr0.202
r_bond_refined_d0.024
r_gen_planes_refined0.011
r_gen_planes_other0.01
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms1732
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing