7WA2

Crystal structure of Bovine Pancreatic Trypsin in complex with 4-Methoxybenzamidine 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
2.346.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.58α = 90
b = 58.3β = 90
c = 67.3γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER X 4M2021-06-22MSINGLE 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
11.525091.40.1770.9877.83.473089711.2
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)
11.521.6188.91.2120.5352.483.68

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 REPLACEMENTTHROUGHOUT1S0R1.5239.8829328153291.430.13570.133460.17753RANDOM13.975
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]
-1.271.130.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.678
r_dihedral_angle_4_deg18.204
r_dihedral_angle_3_deg13.826
r_dihedral_angle_1_deg7.116
r_scangle_other3.832
r_long_range_B_refined3.55
r_long_range_B_other3.506
r_scbond_it3.257
r_scbond_other3.256
r_rigid_bond_restr2.625
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.678
r_dihedral_angle_4_deg18.204
r_dihedral_angle_3_deg13.826
r_dihedral_angle_1_deg7.116
r_scangle_other3.832
r_long_range_B_refined3.55
r_long_range_B_other3.506
r_scbond_it3.257
r_scbond_other3.256
r_rigid_bond_restr2.625
r_mcangle_it2.311
r_mcangle_other2.31
r_mcbond_it1.963
r_mcbond_other1.963
r_angle_refined_deg1.732
r_angle_other_deg1.565
r_chiral_restr0.088
r_bond_refined_d0.016
r_gen_planes_refined0.01
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 Atoms103
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing