8KDU | pdb_00008kdu

Crystal structure of trypsin with its substrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SY3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2910.1 M HEPES (pH=7.8), 16% PEG 3350, and 0.1-0.4 M Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.2946.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.116α = 90
b = 131.116β = 90
c = 71.424γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2021-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.6406

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.316.8399.70.0960.9919.25.610553
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.31000.2490.9511.25.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6SY32.316.831000554299.620.148330.14560.160.197820.2RANDOM12.216
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.016
r_dihedral_angle_3_deg14.32
r_dihedral_angle_1_deg7.848
r_dihedral_angle_4_deg7.117
r_long_range_B_refined4.783
r_long_range_B_other4.782
r_scangle_other2.449
r_angle_refined_deg1.578
r_mcangle_other1.539
r_mcangle_it1.531
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.016
r_dihedral_angle_3_deg14.32
r_dihedral_angle_1_deg7.848
r_dihedral_angle_4_deg7.117
r_long_range_B_refined4.783
r_long_range_B_other4.782
r_scangle_other2.449
r_angle_refined_deg1.578
r_mcangle_other1.539
r_mcangle_it1.531
r_scbond_it1.511
r_scbond_other1.51
r_angle_other_deg1.314
r_mcbond_it0.914
r_mcbond_other0.897
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1629
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing