4TNS | pdb_00004tns

Structure of Pin1 PPIase domain bound with all-trans retinoic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IKG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2970.2 M ammonium sulfate, 0.1 M HEPES pH7-8.5 and 0.9 M-1.4 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
1.6324.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.806α = 90
b = 36.294β = 100.92
c = 51.703γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21ALS5.0.2

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
11.335098.30.04964.93.649111
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)
11.331.3596.70.4652.93.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3IKG1.3342.3446613248197.840.170080.169170.170.186940.19RANDOM14.818
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]
0.13-0.360.23-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.881
r_dihedral_angle_4_deg13.167
r_dihedral_angle_3_deg12.788
r_dihedral_angle_1_deg7.006
r_long_range_B_refined6.382
r_long_range_B_other6.368
r_scangle_other5.539
r_scbond_it3.651
r_scbond_other3.65
r_mcangle_it2.023
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1784
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing