1ZX6

High-resolution crystal structure of yeast Pin3 SH3 domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthew coefficientSolvent content
2.243.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.04α = 90
b = 27.36β = 102.87
c = 24γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.813EMBL/DESY, HamburgX11

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
11.62094.20.0697.9271557155-3-321
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)
11.61.796.80.3122.61.91187

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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: 1oot1.620-37155715535894.310.183470.183470.181570.22089RANDOM21.942
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]
-0.820.362.73-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg27.413
r_dihedral_angle_2_deg26.177
r_dihedral_angle_3_deg10.245
r_dihedral_angle_1_deg5.335
r_scangle_it3.03
r_scbond_it2.536
r_mcangle_it1.605
r_angle_refined_deg1.451
r_mcbond_it1.437
r_angle_other_deg0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg27.413
r_dihedral_angle_2_deg26.177
r_dihedral_angle_3_deg10.245
r_dihedral_angle_1_deg5.335
r_scangle_it3.03
r_scbond_it2.536
r_mcangle_it1.605
r_angle_refined_deg1.451
r_mcbond_it1.437
r_angle_other_deg0.78
r_symmetry_vdw_refined0.379
r_mcbond_other0.338
r_nbd_refined0.191
r_nbtor_refined0.186
r_symmetry_hbond_refined0.174
r_nbd_other0.173
r_symmetry_vdw_other0.164
r_xyhbond_nbd_refined0.147
r_chiral_restr0.096
r_nbtor_other0.085
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms448
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing