4GWT

Structure of racemic Pin1 WW domain cocrystallized with DL-malic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IDHPDB ENTRY 2IDH, CORE BETA-SHEET FRAGMENT (RESI 260-263,268-272,277-279)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298Peptide stock at 5 mg/mL (2.5 mg/mL L-peptide + 2.5 mg/L D-peptide), crystallized from 2.1 M DL-malic acid pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5251.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.985α = 90
b = 65.985β = 90
c = 38.599γ = 90
Symmetry
Space GroupI 41/a

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDBRUKER SMART 60002011-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.2533.321000.06922.8513.34031403141.6
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)
12.252.291000.299.1190

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 2IDH, CORE BETA-SHEET FRAGMENT (RESI 260-263,268-272,277-279)2.2533.324029385717299.970.23930.23940.23840.2599RANDOM39.5828
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]
-0.36-0.360.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.884
r_dihedral_angle_4_deg26.693
r_dihedral_angle_3_deg18.687
r_dihedral_angle_1_deg7.041
r_angle_refined_deg1.495
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms276
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms9

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
HKL-2000data reduction
PHASERphasing