7WA0

Crystal structure of Bovine Pancreatic Trypsin in complex with Benzamidine at Room Temperature


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S0R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293100mM Tris-HCl, 30 %(w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.346.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.58α = 90
b = 58.31β = 90
c = 67.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER X 4M2021-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.000SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.775098.30.1970.9910.035.152123616.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.8898.41.4940.4992.365.11

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 REPLACEMENTTHROUGHOUT1s0r1.7744.0820176102598.330.137880.134610.19901RANDOM18.702
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]
-0.433.16-2.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.448
r_dihedral_angle_4_deg22.196
r_dihedral_angle_3_deg14.632
r_dihedral_angle_1_deg7.248
r_rigid_bond_restr6.751
r_scangle_other5.293
r_long_range_B_refined4.977
r_long_range_B_other4.959
r_scbond_it4.341
r_scbond_other4.339
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.448
r_dihedral_angle_4_deg22.196
r_dihedral_angle_3_deg14.632
r_dihedral_angle_1_deg7.248
r_rigid_bond_restr6.751
r_scangle_other5.293
r_long_range_B_refined4.977
r_long_range_B_other4.959
r_scbond_it4.341
r_scbond_other4.339
r_mcangle_it3.593
r_mcangle_other3.592
r_mcbond_other2.896
r_mcbond_it2.895
r_angle_refined_deg1.772
r_angle_other_deg1.468
r_chiral_restr0.081
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1629
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing