6QIH

Pancreatic Bovine Trypsin with a boronic acid inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A7X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29325% polyethylene glycol 8000 (PEG 8K), 0.2 M ammonium sulfate and 0.1 M sodium cacodylate buffer (pH 6.5)
Crystal Properties
Matthews coefficientSolvent content
2.244.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.49α = 90
b = 56.71β = 90
c = 66.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
11.4242.1599.40.0380.0222.34.53908611.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.599.40.090.0511.94.6

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 REPLACEMENTTHROUGHOUT3A7X1.4242.1537077195599.160.096550.094620.13283RANDOM13.284
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]
-0.05-0.040.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.847
r_sphericity_free32.967
r_dihedral_angle_4_deg17.941
r_rigid_bond_restr14.639
r_dihedral_angle_3_deg11.867
r_sphericity_bonded9.118
r_dihedral_angle_1_deg6.484
r_long_range_B_refined4.226
r_scangle_other3.639
r_long_range_B_other3.562
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.847
r_sphericity_free32.967
r_dihedral_angle_4_deg17.941
r_rigid_bond_restr14.639
r_dihedral_angle_3_deg11.867
r_sphericity_bonded9.118
r_dihedral_angle_1_deg6.484
r_long_range_B_refined4.226
r_scangle_other3.639
r_long_range_B_other3.562
r_scbond_other3.327
r_scbond_it3.326
r_angle_refined_deg2.816
r_angle_other_deg2.24
r_mcangle_other1.877
r_mcangle_it1.875
r_mcbond_it1.549
r_mcbond_other1.546
r_chiral_restr0.192
r_bond_refined_d0.03
r_gen_planes_refined0.015
r_gen_planes_other0.011
r_bond_other_d0.007
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1629
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing