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W354F Yersinia enterocolitica PTPase complexed with tungstate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YPT PDB entry 1YPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Drop: 2uL of protein solution (20mg/mL in 100mM Sodium acetate, 100mM NaCl, 1mM EDTA, 1mM DTT, pH 5.7), 0.5uL of 55mM Sodium tungstate, and 3uL of precipitant solution (12-19% PEG 3350, 0.1M Hepes pH 7.5). Well: 1000uL of precipitant solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.431 α = 90 b = 58.263 β = 90 c = 90.622 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 82 IMAGE PLATE RIGAKU RAXIS IV mirrors 2008-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.69 26.41 96.9 0.035 7.91 31969 31969 15.7
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 1.69 1.75 93.2 0.101 12.8 7.48 3033
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YPT 1.69 26.41 31969 31969 1625 96.91 0.175 0.175 0.173 0.1714 0.207 0.2076 RANDOM 15.738
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] 0.2 0.23 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.414 r_dihedral_angle_4_deg 15.308 r_dihedral_angle_3_deg 10.783 r_dihedral_angle_1_deg 5.594 r_scangle_it 3.483 r_scbond_it 2.122 r_mcangle_it 1.292 r_angle_refined_deg 1.238 r_mcbond_it 0.811 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.414 r_dihedral_angle_4_deg 15.308 r_dihedral_angle_3_deg 10.783 r_dihedral_angle_1_deg 5.594 r_scangle_it 3.483 r_scbond_it 2.122 r_mcangle_it 1.292 r_angle_refined_deg 1.238 r_mcbond_it 0.811 r_nbtor_refined 0.3 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2163 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms 10
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction