3UQV

Bovine trypsin variant X(triplePhe227) 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 DROP729130% PEG8000, 0.2M AMMONIUM SULPHATE, 0.1M IMIDAZOLE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2645.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.502α = 90
b = 84.502β = 90
c = 51.43γ = 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 ANODERIGAKU1.5418

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
12.4301000.1678.77.683128312-3.7
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)
12.42.491000.3884.57.5

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 1V2K2.429.81831283123861000.168670.168670.16560.2553RANDOM21.16
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]
-0.06-0.03-0.060.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.508
r_dihedral_angle_3_deg15.904
r_dihedral_angle_4_deg10.863
r_dihedral_angle_1_deg6.585
r_angle_refined_deg1.672
r_chiral_restr0.114
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.508
r_dihedral_angle_3_deg15.904
r_dihedral_angle_4_deg10.863
r_dihedral_angle_1_deg6.585
r_angle_refined_deg1.672
r_chiral_restr0.114
r_bond_refined_d0.015
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1637
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms49

Software

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