7WB8

Crystal structure of Bovine Pancreatic Trypsin in complex with 5-Methoxytryptamine 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
2.346.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.6α = 90
b = 58.38β = 90
c = 67.2γ = 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
11.385099.30.090.99811.124.974458915.4
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)
11.381.4699.61.2940.5281.64.98

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 REPLACEMENTTHROUGHOUT1S0R1.3844.0742442222499.50.131920.130150.16521RANDOM17.151
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]
-0.141.72-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.34
r_dihedral_angle_4_deg20.981
r_dihedral_angle_3_deg11.746
r_dihedral_angle_1_deg6.977
r_scangle_other4.27
r_long_range_B_refined4.061
r_long_range_B_other4.02
r_scbond_it3.71
r_scbond_other3.708
r_rigid_bond_restr3.675
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.34
r_dihedral_angle_4_deg20.981
r_dihedral_angle_3_deg11.746
r_dihedral_angle_1_deg6.977
r_scangle_other4.27
r_long_range_B_refined4.061
r_long_range_B_other4.02
r_scbond_it3.71
r_scbond_other3.708
r_rigid_bond_restr3.675
r_mcangle_it2.724
r_mcangle_other2.724
r_mcbond_it2.191
r_mcbond_other2.19
r_angle_refined_deg1.867
r_angle_other_deg1.614
r_chiral_restr0.112
r_bond_refined_d0.019
r_gen_planes_refined0.011
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 Atoms118
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing