2J9N

Robotically harvested Trypsin complexed with Benzamidine containing polypeptide mediated crystal contacts


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7295STOCK: 60 MG BOVINE TRYPSIN (SIGMA) PLUS 5 MG BENZAMIDINE (SIGMA) IN 1 ML OF HEPES BUFFER 0.1M PH 7.0 AND 3 MM CACL2. COCKTAIL: 15% PEG 3350 IN 0.1 M HEPES PH 7.0 ALSO CONTAINING 10 MG/ML SALMON SPERM PROTAMINE (SIGMA) DROP: 2 UL STOCK PLUS 2 UL COCKTAIL IN CRYSCHEM PLATES AT 22 DEG C.
Crystal Properties
Matthews coefficientSolvent content
2.0339.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.924α = 90
b = 56.695β = 90
c = 66.054γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray125CCDBruker Platinum 135MIRROR2006-08-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR

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
11.525.0999.30.0524.377.46316412
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)
11.51.5795.90.313.843.32

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1Y5B1.525.0931363166499.80.1550.1540.176RANDOM12.45
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]
-0.10.080.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.002
r_dihedral_angle_4_deg15.038
r_dihedral_angle_3_deg11.833
r_dihedral_angle_1_deg6.466
r_scangle_it4.886
r_scbond_it3.451
r_mcangle_it2.691
r_mcbond_it1.739
r_angle_refined_deg1.324
r_angle_other_deg0.892
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.002
r_dihedral_angle_4_deg15.038
r_dihedral_angle_3_deg11.833
r_dihedral_angle_1_deg6.466
r_scangle_it4.886
r_scbond_it3.451
r_mcangle_it2.691
r_mcbond_it1.739
r_angle_refined_deg1.324
r_angle_other_deg0.892
r_symmetry_vdw_other0.247
r_nbd_other0.193
r_nbd_refined0.191
r_nbtor_refined0.174
r_symmetry_vdw_refined0.165
r_symmetry_hbond_refined0.149
r_xyhbond_nbd_refined0.139
r_chiral_restr0.086
r_nbtor_other0.086
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1708
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms18

Software

Software
Software NamePurpose
BRUKERdata reduction
SCALEPACKdata scaling
EPMRphasing
SHAKEANDWARPphasing
REFMACrefinement