5F03

TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin-house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320% PEG 10000, 0.1 M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.6753.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.34α = 90
b = 78.34β = 90
c = 165.95γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2006-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.5418

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
11.9467.8898.80.0960.01035.443956
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)
11.942.0693.20.2494.785.2

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTin-house structure1.9467.8841738221899.390.157260.154940.20026RANDOM15.628
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]
0.330.160.33-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.519
r_dihedral_angle_3_deg14.031
r_dihedral_angle_4_deg12.039
r_dihedral_angle_1_deg6.233
r_scangle_it2.42
r_scbond_it1.675
r_angle_refined_deg1.442
r_mcangle_it1.074
r_mcbond_it0.68
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.519
r_dihedral_angle_3_deg14.031
r_dihedral_angle_4_deg12.039
r_dihedral_angle_1_deg6.233
r_scangle_it2.42
r_scbond_it1.675
r_angle_refined_deg1.442
r_mcangle_it1.074
r_mcbond_it0.68
r_nbtor_refined0.314
r_nbd_refined0.209
r_symmetry_vdw_refined0.204
r_xyhbond_nbd_refined0.157
r_symmetry_hbond_refined0.134
r_chiral_restr0.1
r_bond_refined_d0.012
r_gen_planes_refined0.006
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_refined
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_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 Atoms3831
Nucleic Acid Atoms
Solvent Atoms689
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XPREPdata scaling
REFMACphasing