3PLP

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 DROP829320% PEG 8000, 0.1M IMIDAZOLE, 0.2M AMMONIUM SULPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0439.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.096α = 90
b = 55.096β = 90
c = 108.881γ = 120
Symmetry
Space GroupP 31 2 1

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
11.633099.90.06920.78.6245762457619
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)
11.631.6999.90.2695.32392

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 1V2K1.6328.89245762457624861000.172230.172230.170260.21097RANDOM17.331
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]
0.530.270.53-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.972
r_dihedral_angle_4_deg17.34
r_dihedral_angle_3_deg10.666
r_dihedral_angle_1_deg6.38
r_scangle_it3.092
r_scbond_it2.033
r_angle_refined_deg1.416
r_mcangle_it1.224
r_mcbond_it0.687
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.972
r_dihedral_angle_4_deg17.34
r_dihedral_angle_3_deg10.666
r_dihedral_angle_1_deg6.38
r_scangle_it3.092
r_scbond_it2.033
r_angle_refined_deg1.416
r_mcangle_it1.224
r_mcbond_it0.687
r_chiral_restr0.102
r_bond_refined_d0.011
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1633
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms35

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
SCALAdata scaling