3OOB

Structural and functional insights of directly targeting Pin1 by Epigallocatechin-3-gallate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52772.2-2.7M Ammonium Sulfate, 1% PEG400, 1mM Dithiothreitol, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0359.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.409α = 90
b = 69.409β = 90
c = 79.268γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMirrors2007-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.99188APS23-ID-D

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
11.93099.90.0958.910.817999
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)
11.91.97990.49810.41744

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.8928.11796790299.760.19180.18980.2316RANDOM30.8833
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]
2.221.112.22-3.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.549
r_dihedral_angle_4_deg21.693
r_dihedral_angle_3_deg14.168
r_dihedral_angle_1_deg6.218
r_scangle_it2.952
r_scbond_it1.941
r_mcangle_it1.334
r_angle_refined_deg1.317
r_mcbond_it0.833
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.549
r_dihedral_angle_4_deg21.693
r_dihedral_angle_3_deg14.168
r_dihedral_angle_1_deg6.218
r_scangle_it2.952
r_scbond_it1.941
r_mcangle_it1.334
r_angle_refined_deg1.317
r_mcbond_it0.833
r_nbtor_refined0.307
r_nbd_refined0.194
r_symmetry_vdw_refined0.188
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.122
r_chiral_restr0.092
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1165
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms111

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOLREPphasing