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Crystal structure of protein tyrosine phosphatase from Entamoeba histolytica with a phosphotyrosine crude mimic HEPES molecule in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XWW PDB entry 1xww
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 ProPlex condition F1, 0.1 M Hepes pH 7.0, 20% PEG 8000, 25% glycerol as cryo-protectant, 26.1 mg/mL protein, 0.1 mg/mL chymotrypsin, crystal tracking ID 203694f1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.07 40.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.579 α = 90 b = 70.409 β = 90 c = 79.189 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 2009-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.9765 ALS 5.0.3
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 2.2 45.93 98.6 0.14 7.7 8.1 17494
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 2.2 2.28 89.5 0.492 2.43 5.7 1539
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1xww 2.2 45.93 17445 887 98.45 0.206 0.204 0.2022 0.254 0.2491 RANDOM 36.713
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] -2.71 -0.15 2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.578 r_dihedral_angle_3_deg 14.642 r_dihedral_angle_4_deg 13.839 r_dihedral_angle_1_deg 5.64 r_scangle_it 2.542 r_scbond_it 1.541 r_angle_refined_deg 1.211 r_mcangle_it 1.095 r_mcbond_it 0.576 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.578 r_dihedral_angle_3_deg 14.642 r_dihedral_angle_4_deg 13.839 r_dihedral_angle_1_deg 5.64 r_scangle_it 2.542 r_scbond_it 1.541 r_angle_refined_deg 1.211 r_mcangle_it 1.095 r_mcbond_it 0.576 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2524 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling