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Structure of Ygr203w, a yeast protein tyrosine phosphatase of the Rhodanese family
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 0.1 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 = 74.382 α = 90 b = 72.025 β = 103.6 c = 53.514 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 Mirrors 2008-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.75 50 98.7 0.08 25.682 3.6 27702 27354 19.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.81 89.3 0.295 2.6 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT none 1.8 36.01 24128 1281 99.7 0.16808 0.16575 0.1992 0.21064 0.2413 RANDOM 21.415
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.046 r_dihedral_angle_3_deg 15.365 r_dihedral_angle_4_deg 14.072 r_dihedral_angle_1_deg 5.372 r_scangle_it 3.899 r_scbond_it 2.863 r_angle_refined_deg 1.564 r_mcangle_it 1.539 r_mcbond_it 1.236 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.046 r_dihedral_angle_3_deg 15.365 r_dihedral_angle_4_deg 14.072 r_dihedral_angle_1_deg 5.372 r_scangle_it 3.899 r_scbond_it 2.863 r_angle_refined_deg 1.564 r_mcangle_it 1.539 r_mcbond_it 1.236 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.279 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 Atoms Number Protein Atoms 2462 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 42
Software Software Software Name Purpose SBC-Collect data collection SHELXCD phasing SHELXE model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling