3A85 | pdb_00003a85

Crystal Structure of Trypsin complexed with (E)-2-(4-carbamimidoylbenzylideneaminooxy)acetic acid (soaking 15 seconds)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A7T 

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
2.1843.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.954α = 90
b = 56.906β = 90
c = 66.142γ = 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
11.755099.50.0340.03440.85.7-3
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)
1.751.8194.90.0940.09411.84.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3A7T1.7519.6219866106099.690.15730.155880.160.183290.16RANDOM15.429
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]
-0.030.17-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.964
r_dihedral_angle_4_deg18.187
r_dihedral_angle_3_deg11.927
r_dihedral_angle_1_deg5.979
r_scangle_it3.045
r_scbond_it1.884
r_angle_refined_deg1.279
r_mcangle_it1.179
r_mcbond_it0.681
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.964
r_dihedral_angle_4_deg18.187
r_dihedral_angle_3_deg11.927
r_dihedral_angle_1_deg5.979
r_scangle_it3.045
r_scbond_it1.884
r_angle_refined_deg1.279
r_mcangle_it1.179
r_mcbond_it0.681
r_nbtor_refined0.298
r_symmetry_vdw_refined0.229
r_nbd_refined0.194
r_symmetry_hbond_refined0.192
r_metal_ion_refined0.115
r_xyhbond_nbd_refined0.112
r_chiral_restr0.09
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 Atoms301
Heterogen Atoms29

Software

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