☰ Navigation Tabs
W354F Yersinia enterocolitica PTPase complexed with divanadate
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 vanadate, 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 2.13 42.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.196 α = 90 b = 58.191 β = 90 c = 90.347 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 100 CCD ADSC QUANTUM 315 mirrors 2008-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
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 1.42 30 98.8 0.065 30.828 8.3 54027 54027 17.9
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 1.42 1.47 89.5 0.271 4.9 4789
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 1.42 29.1 53940 53940 2772 99.17 0.174 0.174 0.173 0.1721 0.196 0.1974 RANDOM 21.046
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] 0.18 0.37 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.166 r_dihedral_angle_4_deg 16.188 r_dihedral_angle_3_deg 11.192 r_dihedral_angle_1_deg 6.113 r_scangle_it 2.996 r_scbond_it 1.978 r_angle_refined_deg 1.353 r_mcangle_it 1.348 r_mcbond_it 0.878 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.166 r_dihedral_angle_4_deg 16.188 r_dihedral_angle_3_deg 11.192 r_dihedral_angle_1_deg 6.113 r_scangle_it 2.996 r_scbond_it 1.978 r_angle_refined_deg 1.353 r_mcangle_it 1.348 r_mcbond_it 0.878 r_nbtor_refined 0.3 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.158 r_symmetry_hbond_refined 0.111 r_xyhbond_nbd_refined 0.089 r_chiral_restr 0.084 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2163 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing