3KCE

Structure-guided design of alpha-amino acid-derived Pin1 inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PINPDB ENTRY 1PIN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52772.2M Ammonium sulphate, 0.1M HEPES buffer, 1% PEG 400, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.9157.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.354α = 90
b = 68.354β = 90
c = 79.849γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2009-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.927.895.90.048.33.1167391673911
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)
1.91.9797.90.2392.52.71436

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1PIN1.925158821588285295.910.216720.216720.214750.25376RANDOM31.905
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]
1.460.731.46-2.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.18
r_dihedral_angle_4_deg18.205
r_dihedral_angle_3_deg14.404
r_dihedral_angle_1_deg6.395
r_scangle_it3.88
r_scbond_it2.614
r_mcangle_it1.563
r_angle_refined_deg1.466
r_mcbond_it0.963
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.18
r_dihedral_angle_4_deg18.205
r_dihedral_angle_3_deg14.404
r_dihedral_angle_1_deg6.395
r_scangle_it3.88
r_scbond_it2.614
r_mcangle_it1.563
r_angle_refined_deg1.466
r_mcbond_it0.963
r_nbtor_refined0.303
r_symmetry_hbond_refined0.267
r_nbd_refined0.203
r_symmetry_vdw_refined0.202
r_xyhbond_nbd_refined0.136
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1154
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms37

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling