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Crystal structure of human low molecular weight protein tyrosine phosphatase (LMPTP) type A complexed with MES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 293 20% PEG 3350, 200 mM NaCl, 40 mM MES
Crystal Properties Matthews coefficient Solvent content 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.905 α = 90 b = 55.018 β = 90 c = 96.423 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 2015-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.0781 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.36 33.9 97.8 0.039 0.999 25 5.9 38952
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 1.36 1.38 72.7 0.227 1.6
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 5JNR 1.45 33.9 31159 1610 99.83 0.1362 0.1346 0.1344 0.1658 0.1653 RANDOM 15.964
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] -0.07 0.03 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.386 r_dihedral_angle_4_deg 15.166 r_dihedral_angle_3_deg 11.764 r_dihedral_angle_1_deg 6.296 r_angle_refined_deg 3.023 r_mcangle_it 2.306 r_mcbond_it 1.49 r_mcbond_other 1.478 r_angle_other_deg 1.275 r_chiral_restr 0.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.386 r_dihedral_angle_4_deg 15.166 r_dihedral_angle_3_deg 11.764 r_dihedral_angle_1_deg 6.296 r_angle_refined_deg 3.023 r_mcangle_it 2.306 r_mcbond_it 1.49 r_mcbond_other 1.478 r_angle_other_deg 1.275 r_chiral_restr 0.387 r_bond_refined_d 0.036 r_gen_planes_refined 0.016 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1232 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 24
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing