3A81

Crystal Structure of Trypsin complexed with (E)-4-((2-nicotinoylhydrazono)methyl)benzimidamide (soaking 8 hours)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.1M Tris-HCl, 30% PEG 3350, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2845.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.61α = 90
b = 58.363β = 90
c = 66.642γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VIIMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.785097.40.0430.04337.97.1-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.86920.070.07216.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3A7T1.7819.9419445104499.950.146030.144140.18306RANDOM17.522
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]
0.22-0.21-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.612
r_dihedral_angle_4_deg16.666
r_dihedral_angle_3_deg11.252
r_dihedral_angle_1_deg6.194
r_scangle_it2.611
r_scbond_it1.756
r_angle_refined_deg1.178
r_mcangle_it1.095
r_mcbond_it0.639
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.612
r_dihedral_angle_4_deg16.666
r_dihedral_angle_3_deg11.252
r_dihedral_angle_1_deg6.194
r_scangle_it2.611
r_scbond_it1.756
r_angle_refined_deg1.178
r_mcangle_it1.095
r_mcbond_it0.639
r_nbtor_refined0.301
r_symmetry_hbond_refined0.241
r_nbd_refined0.19
r_symmetry_vdw_refined0.153
r_metal_ion_refined0.146
r_xyhbond_nbd_refined0.114
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms1629
Nucleic Acid Atoms
Solvent Atoms377
Heterogen Atoms37

Software

Software
Software NamePurpose
LAFIREmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
LAFIREphasing