3KAF

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
2.8656.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.937α = 90
b = 67.937β = 90
c = 79.247γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2006-11-03MSINGLE 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
12.327.696.20.0814.62.99395939511
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)
2.32.3899.80.4381.32.8885

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 DIFFRACTIONMIRTHROUGHOUTPDB ENTRY 1PIN2.327.6893945296.050.230480.226640.31195RANDOM46.677
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]
2.261.132.26-3.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.744
r_dihedral_angle_4_deg24.382
r_dihedral_angle_3_deg17.609
r_dihedral_angle_1_deg7.527
r_scangle_it4.157
r_scbond_it2.6
r_mcangle_it1.983
r_angle_refined_deg1.908
r_mcbond_it1.094
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.744
r_dihedral_angle_4_deg24.382
r_dihedral_angle_3_deg17.609
r_dihedral_angle_1_deg7.527
r_scangle_it4.157
r_scbond_it2.6
r_mcangle_it1.983
r_angle_refined_deg1.908
r_mcbond_it1.094
r_chiral_restr0.117
r_bond_refined_d0.019
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1152
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms26

Software

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