3KAH

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
3.0159.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.893α = 90
b = 69.893β = 90
c = 79.027γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2006-12-04MSINGLE 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
12.324.291.60.0656.22.89435943511
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)
2.32.3895.30.3091.92.5817

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1PIN2.324.15848494791.630.202320.194380.2735RANDOM32.647
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]
0.240.120.24-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.482
r_dihedral_angle_4_deg19.374
r_dihedral_angle_3_deg16.773
r_dihedral_angle_1_deg7.564
r_scangle_it4.785
r_scbond_it2.983
r_angle_refined_deg1.776
r_mcangle_it1.755
r_mcbond_it0.906
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.482
r_dihedral_angle_4_deg19.374
r_dihedral_angle_3_deg16.773
r_dihedral_angle_1_deg7.564
r_scangle_it4.785
r_scbond_it2.983
r_angle_refined_deg1.776
r_mcangle_it1.755
r_mcbond_it0.906
r_chiral_restr0.102
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1156
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms53

Software

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