3V13

Bovine trypsin variant X(tripleGlu217Phe227) 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 DROP729320% PEG8000, 0.2M AMMONIUM SULPHATE, 0.1M IMIDAZOLE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6353.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.813α = 90
b = 81.813β = 90
c = 63.865γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.542

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
11.6370.891000.11810.68.93043930439-3.7

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 1V2K1.6370.893040930409153899.970.147840.147840.145630.17539RANDOM14.917
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.892
r_dihedral_angle_4_deg12.722
r_dihedral_angle_3_deg11.61
r_dihedral_angle_1_deg6.543
r_scangle_it2.659
r_scbond_it1.743
r_angle_refined_deg1.489
r_mcangle_it1.142
r_mcbond_it0.678
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.892
r_dihedral_angle_4_deg12.722
r_dihedral_angle_3_deg11.61
r_dihedral_angle_1_deg6.543
r_scangle_it2.659
r_scbond_it1.743
r_angle_refined_deg1.489
r_mcangle_it1.142
r_mcbond_it0.678
r_chiral_restr0.092
r_bond_refined_d0.016
r_gen_planes_refined0.008
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 Atoms1641
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms61

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling