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Crystal structure of Low Molecular Weight Protein Tyrosine Phosphatase isoform A complexed with benzylphosphonic 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, HANGING DROP 7 291 32% (w/v) PEG 5000, 0.1 M malic acid:Tris, molar ratio 1:2, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.36 47.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.088 α = 90 b = 54.287 β = 90 c = 97.468 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 APEX II CCD 2013-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 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 2.4 27.8 99.7 0.1455 16.34 11.84 7097
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 2.4 2.45 100 0.5618 2.94 11.58
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 5PNT 2.41 27.8 6641 325 99.26 0.21875 0.21479 0.2204 0.30148 0.3024 RANDOM 35.003
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] 1.77 -1.7 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.456 r_dihedral_angle_4_deg 20.462 r_dihedral_angle_3_deg 15.492 r_dihedral_angle_1_deg 6.825 r_long_range_B_refined 4.635 r_long_range_B_other 4.634 r_mcangle_it 2.513 r_mcangle_other 2.512 r_scangle_other 2.334 r_angle_refined_deg 1.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.456 r_dihedral_angle_4_deg 20.462 r_dihedral_angle_3_deg 15.492 r_dihedral_angle_1_deg 6.825 r_long_range_B_refined 4.635 r_long_range_B_other 4.634 r_mcangle_it 2.513 r_mcangle_other 2.512 r_scangle_other 2.334 r_angle_refined_deg 1.562 r_mcbond_it 1.502 r_mcbond_other 1.502 r_scbond_it 1.393 r_scbond_other 1.393 r_angle_other_deg 0.89 r_chiral_restr 0.077 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1249 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 11
Software Software Software Name Purpose APEX data collection APEX data reduction APEX data scaling PHASER phasing REFMAC refinement