3Q00

Bovine trypsin variant X(tripleGlu217Ile227) in complex with small molecule inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829330% PEG8000, 0.2M AMMONIUM SULPHATE, 0.1M IMIDAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4750.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.04α = 90
b = 54.04β = 90
c = 137.08γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+mirrorsMSINGLE 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
11.71699.970.0516.73.7254872548718

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 REPLACEMENTTHROUGHOUT1V2K1.715.62548725487198199.970.174490.174490.173930.20845RANDOM18.594
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]
0.530.260.53-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.288
r_dihedral_angle_4_deg14.386
r_dihedral_angle_3_deg13.455
r_dihedral_angle_1_deg6.574
r_scangle_it5.267
r_scbond_it4.009
r_mcangle_it3.854
r_mcbond_it3.287
r_angle_refined_deg1.431
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.288
r_dihedral_angle_4_deg14.386
r_dihedral_angle_3_deg13.455
r_dihedral_angle_1_deg6.574
r_scangle_it5.267
r_scbond_it4.009
r_mcangle_it3.854
r_mcbond_it3.287
r_angle_refined_deg1.431
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1636
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms57

Software

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