☰ Navigation Tabs
Engineered protein tyrosine phosphatase beta catalytic domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.85 298 21% PEG 8000, 200 mM MgCl2, 1% BME, 0.1% BOG, 1mM DTT, 80 mM Na Citrate, pH 7.85, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 38.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.314 α = 90 b = 70.775 β = 92.52 c = 49.846 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARRESEARCH 2006-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-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 1.4 33.67 92.5 0.028 20.2 2.6 48397 48397
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) 1.4 1.5 69.4 0.21 4.87 1.4
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 (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 2HC1 1.4 33.67 48397 45933 2464 92.51 0.14571 0.14391 0.1416 0.17892 0.176 RANDOM 19.055
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] 0.67 0.05 -0.32 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_sphericity_free 16.373 r_dihedral_angle_4_deg 15.582 r_dihedral_angle_3_deg 14.775 r_sphericity_bonded 10.465 r_scangle_it 6.959 r_dihedral_angle_1_deg 6.896 r_scbond_it 5.308 r_mcangle_it 4.138 r_rigid_bond_restr 3.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_sphericity_free 16.373 r_dihedral_angle_4_deg 15.582 r_dihedral_angle_3_deg 14.775 r_sphericity_bonded 10.465 r_scangle_it 6.959 r_dihedral_angle_1_deg 6.896 r_scbond_it 5.308 r_mcangle_it 4.138 r_rigid_bond_restr 3.487 r_mcbond_it 3.024 r_angle_refined_deg 1.206 r_symmetry_vdw_refined 0.375 r_nbtor_refined 0.319 r_nbd_refined 0.26 r_xyhbond_nbd_refined 0.206 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.102 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2488 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data scaling AMoRE phasing