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Crystal structure of Low Molecular Weight Protein Tyrosine Phosphatase isoform A complexed with phenylmethanesulfonic 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 6.5 291 26% (w/v) PEG 5000, 0.2 M ammonium sulfate, 0.2 M MES buffer pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.46 49.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.75 α = 90 b = 55.23 β = 90 c = 97.8 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 225 mm CCD 2011-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.459 LNLS W01B-MX2
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 2.1 32.6 98.2 0.085 9.2 4 10699
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 2.1 2.21 97.3 0.508 2.2 4
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 2.1 28.07 9846 796 97.59 0.1832 0.17909 0.1872 0.23511 0.2438 RANDOM 41.696
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] -0.45 -0.18 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.888 r_dihedral_angle_4_deg 18.317 r_dihedral_angle_3_deg 13.881 r_dihedral_angle_1_deg 6.448 r_long_range_B_refined 6.413 r_long_range_B_other 6.411 r_scangle_other 4.204 r_mcangle_other 3.294 r_mcangle_it 3.288 r_scbond_it 2.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.888 r_dihedral_angle_4_deg 18.317 r_dihedral_angle_3_deg 13.881 r_dihedral_angle_1_deg 6.448 r_long_range_B_refined 6.413 r_long_range_B_other 6.411 r_scangle_other 4.204 r_mcangle_other 3.294 r_mcangle_it 3.288 r_scbond_it 2.813 r_scbond_other 2.812 r_mcbond_it 2.304 r_mcbond_other 2.258 r_angle_refined_deg 1.66 r_angle_other_deg 0.873 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 1230 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing