3A8A

Crystal Structure of Trypsin complexed with 4-formylbenzimidamide and aniline


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
2.2645.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.316α = 90
b = 58.433β = 90
c = 66.316γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
11.450970.0390.03935.96-3
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)
1.41.4598.60.0690.06923.26.8

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 REPLACEMENTTHROUGHOUT3A7T1.416.837897196997.320.166560.165520.18666RANDOM12.993
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]
0.12-0.130.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.317
r_dihedral_angle_4_deg16.719
r_dihedral_angle_3_deg10.553
r_dihedral_angle_1_deg6.135
r_scangle_it2.231
r_scbond_it1.517
r_angle_refined_deg1.146
r_mcangle_it0.968
r_mcbond_it0.573
r_nbd_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.317
r_dihedral_angle_4_deg16.719
r_dihedral_angle_3_deg10.553
r_dihedral_angle_1_deg6.135
r_scangle_it2.231
r_scbond_it1.517
r_angle_refined_deg1.146
r_mcangle_it0.968
r_mcbond_it0.573
r_nbd_refined0.306
r_nbtor_refined0.3
r_xyhbond_nbd_refined0.242
r_symmetry_vdw_refined0.228
r_symmetry_hbond_refined0.14
r_metal_ion_refined0.131
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.004
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 Atoms426
Heterogen Atoms29

Software

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