4MPU

Human beta-tryptase co-crystal structure with (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-8-hydroxy-6-(1-hydroxycyclobutyl)-5,7-dioxaspiro[3.4]octane-6,8-dicarboxamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.629830% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, individual monocrystals equilibrated with 30% PEG1500, 0.1 M MES, pH 5.5, 0.2 M ammonium sulfate and soaked 20 hours in same solution supplemented with compound 2A, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6553.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.157α = 90
b = 78.157β = 90
c = 165.039γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2011-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

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
11.6495099.80.068134.27113070669

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.64919.86758867095357599.270.180160.180160.178240.21613RANDOM24.978
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.13
r_dihedral_angle_3_deg14.06
r_dihedral_angle_4_deg13.332
r_dihedral_angle_1_deg6.799
r_angle_other_deg3.646
r_angle_refined_deg2.9
r_chiral_restr0.149
r_gen_planes_other0.046
r_bond_refined_d0.024
r_gen_planes_refined0.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.13
r_dihedral_angle_3_deg14.06
r_dihedral_angle_4_deg13.332
r_dihedral_angle_1_deg6.799
r_angle_other_deg3.646
r_angle_refined_deg2.9
r_chiral_restr0.149
r_gen_planes_other0.046
r_bond_refined_d0.024
r_gen_planes_refined0.016
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3832
Nucleic Acid Atoms
Solvent Atoms515
Heterogen Atoms134

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling