3UOP

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 DROP829320% PEG8000, 0.1M AMMONIUM SULPHATE, 0.1M IMIDAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.957.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.089α = 90
b = 55.089β = 90
c = 154.868γ = 120
Symmetry
Space GroupP 32 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 ANODERIGAKU1.542

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
11.6935.0488.60.08612.65.62805928059-3.7
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)
11.691.75240.2822.51.5

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 1V2K1.6935.04280582805822101000.18560.18560.180370.22001RANDOM23.5569
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]
1.080.541.08-1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.373
r_dihedral_angle_4_deg14.267
r_dihedral_angle_3_deg11.761
r_dihedral_angle_1_deg6.467
r_scangle_it2.919
r_scbond_it1.985
r_angle_refined_deg1.349
r_mcangle_it1.209
r_mcbond_it0.684
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.373
r_dihedral_angle_4_deg14.267
r_dihedral_angle_3_deg11.761
r_dihedral_angle_1_deg6.467
r_scangle_it2.919
r_scbond_it1.985
r_angle_refined_deg1.349
r_mcangle_it1.209
r_mcbond_it0.684
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1636
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms60

Software

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