3F4A

Structure of Ygr203w, a yeast protein tyrosine phosphatase of the Rhodanese family


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52950.1 M Tris 8,5, 1.5 M LiSO4 plus 0.015 mg/ml trypsin. Cryoprotected with N-paratone oil, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.382α = 90
b = 72.025β = 103.6
c = 53.514γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2008-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97929APS19-ID

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
11.755098.70.0825.6823.6277022735419.6
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)
1.751.8189.30.2952.62.6

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 DIFFRACTIONSADTHROUGHOUTnone1.836.0124128128199.70.168080.165750.21064RANDOM21.415
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.046
r_dihedral_angle_3_deg15.365
r_dihedral_angle_4_deg14.072
r_dihedral_angle_1_deg5.372
r_scangle_it3.899
r_scbond_it2.863
r_angle_refined_deg1.564
r_mcangle_it1.539
r_mcbond_it1.236
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.046
r_dihedral_angle_3_deg15.365
r_dihedral_angle_4_deg14.072
r_dihedral_angle_1_deg5.372
r_scangle_it3.899
r_scbond_it2.863
r_angle_refined_deg1.564
r_mcangle_it1.539
r_mcbond_it1.236
r_nbtor_refined0.312
r_symmetry_vdw_refined0.279
r_symmetry_hbond_refined0.236
r_nbd_refined0.211
r_xyhbond_nbd_refined0.164
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2462
Nucleic Acid Atoms
Solvent Atoms312
Heterogen Atoms42

Software

Software
Software NamePurpose
SBC-Collectdata collection
SHELXCDphasing
SHELXEmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling