3TDB

Human Pin1 bound to trans peptidomimetic inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52771.9-2.2 M ammonium sulfate, 1% PEG400 at pH 7.5 in 50 mM HEPES buffer, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1360.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.273α = 90
b = 69.273β = 90
c = 79.657γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMACSCIENCE DIP1002004-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEMACSCIENCE1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.265097.51048810226-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.262.3485.90.3015.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.26747.951047210205103797.450.22120.21680.2561RANDOM29.9775
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]
0.80.40.8-1.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.54
r_dihedral_angle_4_deg17.339
r_dihedral_angle_3_deg15.647
r_dihedral_angle_1_deg6.274
r_scangle_it2.865
r_scbond_it1.859
r_angle_refined_deg1.516
r_mcangle_it1.296
r_mcbond_it0.777
r_nbtor_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.54
r_dihedral_angle_4_deg17.339
r_dihedral_angle_3_deg15.647
r_dihedral_angle_1_deg6.274
r_scangle_it2.865
r_scbond_it1.859
r_angle_refined_deg1.516
r_mcangle_it1.296
r_mcbond_it0.777
r_nbtor_refined0.293
r_symmetry_hbond_refined0.205
r_nbd_refined0.203
r_xyhbond_nbd_refined0.162
r_symmetry_vdw_refined0.139
r_chiral_restr0.097
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1164
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms63

Software

Software
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction