9KK5 | pdb_00009kk5

Crystal Structure of Bovine Pancreatic Trypsin in Complex with Pyridoxal


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
2.2344.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.559α = 90
b = 58.123β = 90
c = 65.626γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSBRUKER PHOTON 1002023-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 VENTURE1.5406

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1220.9999.90.08814.83.414645
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)
1220.3683

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 REPLACEMENTTHROUGHOUT6SY3220.991391469099.790.171050.167990.17990.231960.2332RANDOM11.07
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]
-0.470.260.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.242
r_dihedral_angle_4_deg17.956
r_dihedral_angle_3_deg13.974
r_dihedral_angle_1_deg7.886
r_long_range_B_refined5.209
r_long_range_B_other4.868
r_scangle_other1.774
r_mcangle_it1.616
r_mcangle_other1.615
r_angle_refined_deg1.518
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.242
r_dihedral_angle_4_deg17.956
r_dihedral_angle_3_deg13.974
r_dihedral_angle_1_deg7.886
r_long_range_B_refined5.209
r_long_range_B_other4.868
r_scangle_other1.774
r_mcangle_it1.616
r_mcangle_other1.615
r_angle_refined_deg1.518
r_angle_other_deg1.361
r_scbond_it1.1
r_scbond_other1.095
r_mcbond_it0.959
r_mcbond_other0.959
r_chiral_restr0.063
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms282
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing