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Crystal structure of the A isoform of human cytoplasmic protein tyrosine phosphatase (HCPTP-A) in complex with 1-naphtylacetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5PNT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 22.5% PEG 3350, 0.1M TRIS pH 7.5, 10mM 1-naphthylacetic acid, 2% isopropanol, 1mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.46 α = 90 b = 56.09 β = 90 c = 95.99 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 MARMOSAIC 300 mm CCD SI(111) double crystal monochromator 2009-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.968 APS 23-ID-D
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 1.5 50 99.03 0.127 15.02 12.2 27538 27270 1 122.9 19.291
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 1.5 1.55 96.2 0.389 4.71 5.9 2738
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 5PNT 1.5 32.46 1 27537 27270 1464 99.03 0.175 0.174 0.1823 0.203 0.2145 RANDOM 19.291
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] -0.13 0.19 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.692 r_dihedral_angle_4_deg 19.096 r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 5.336 r_sphericity_free 3.017 r_scangle_it 2.933 r_sphericity_bonded 2.152 r_scbond_it 1.961 r_mcangle_it 1.362 r_angle_refined_deg 1.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.692 r_dihedral_angle_4_deg 19.096 r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 5.336 r_sphericity_free 3.017 r_scangle_it 2.933 r_sphericity_bonded 2.152 r_scbond_it 1.961 r_mcangle_it 1.362 r_angle_refined_deg 1.164 r_rigid_bond_restr 1.04 r_mcbond_it 0.794 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1229 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 14
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling