3PM3

Bovine trypsin variant X(tripleIle227) in complex with small molecule inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V2KPDB ENTRY 1V2K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829330% PEG 8000, 0.1M IMIDAZOLE, 0.2M AMMONIUM SULPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0539.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.502α = 90
b = 54.502β = 90
c = 111.708γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
11.525093.90.1725.64.5298352983513
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)
11.521.57610.5471.32.91890

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1V2K1.53502946327979148498.580.153540.153540.153510.18126RANDOM14.447
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]
-0.12-0.06-0.120.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.99
r_dihedral_angle_4_deg21.015
r_dihedral_angle_3_deg10.957
r_dihedral_angle_1_deg6.58
r_scangle_it2.862
r_scbond_it1.931
r_angle_refined_deg1.532
r_mcangle_it1.293
r_mcbond_it0.733
r_chiral_restr0.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.99
r_dihedral_angle_4_deg21.015
r_dihedral_angle_3_deg10.957
r_dihedral_angle_1_deg6.58
r_scangle_it2.862
r_scbond_it1.931
r_angle_refined_deg1.532
r_mcangle_it1.293
r_mcbond_it0.733
r_chiral_restr0.258
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1633
Nucleic Acid Atoms
Solvent Atoms371
Heterogen Atoms63

Software

Software
Software NamePurpose
MxCuBEdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling