9KK4 | pdb_00009kk4

Crystal Structure of Bovine Pancreatic Trypsin in Complex with Pyridoxine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M HEPES (pH =7.5), 0.1-0.4 M Li2SO4, and PEG 16%
Crystal Properties
Matthews coefficientSolvent content
2.1843.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.045α = 90
b = 57.75β = 90
c = 65.676γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSBRUKER PHOTON 1002021-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 VENTURE1.5406

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.3519.7499.70.18311.26.88986
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.440.4555.4

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 REPLACEMENTTHROUGHOUT6SY32.3519.74850245099.590.202080.199030.20960.260060.2303RANDOM14.572
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]
0.190.36-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.774
r_dihedral_angle_2_deg9.73
r_dihedral_angle_1_deg7.957
r_long_range_B_refined3.433
r_long_range_B_other3.433
r_scangle_other1.824
r_mcangle_it1.707
r_mcangle_other1.707
r_angle_refined_deg1.407
r_scbond_it1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.774
r_dihedral_angle_2_deg9.73
r_dihedral_angle_1_deg7.957
r_long_range_B_refined3.433
r_long_range_B_other3.433
r_scangle_other1.824
r_mcangle_it1.707
r_mcangle_other1.707
r_angle_refined_deg1.407
r_scbond_it1.07
r_scbond_other1.069
r_mcbond_it1.007
r_mcbond_other1.007
r_angle_other_deg0.506
r_chiral_restr0.065
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms1641
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing