7WB7

Crystal structure of Bovine Pancreatic Trypsin in complex with Serotonin 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
2.2946.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.66α = 90
b = 58.17β = 90
c = 67.34γ = 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
11.455098.50.1550.997.844.753821314
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)
11.451.541.2070.5351.8

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 REPLACEMENTTHROUGHOUT1S0R1.4544.0236240192598.460.132840.130730.17218RANDOM15.922
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]
-0.521.42-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.936
r_dihedral_angle_4_deg20.373
r_dihedral_angle_3_deg14.304
r_dihedral_angle_1_deg7.065
r_scangle_other5.621
r_scbond_it4.681
r_scbond_other4.678
r_long_range_B_refined4.307
r_long_range_B_other4.266
r_rigid_bond_restr2.738
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.936
r_dihedral_angle_4_deg20.373
r_dihedral_angle_3_deg14.304
r_dihedral_angle_1_deg7.065
r_scangle_other5.621
r_scbond_it4.681
r_scbond_other4.678
r_long_range_B_refined4.307
r_long_range_B_other4.266
r_rigid_bond_restr2.738
r_mcangle_it2.6
r_mcangle_other2.6
r_mcbond_it2.075
r_mcbond_other2.073
r_angle_refined_deg1.746
r_angle_other_deg1.59
r_chiral_restr0.095
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 Atoms129
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing