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Crystal structure of human low molecular weight protein tyrosine phosphatase (LMPTP) type A complexed with phosphate
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 8 293 25% PEG 3350K, 200 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.21 α = 90 b = 55.09 β = 90 c = 95.2 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 1.74 55.09 99.8 0.108 0.993 9.1 6.4 18220
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 1.74 1.77 99.9 0.607 5.4
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 5JNR 1.8 47.68 15543 774 99.71 0.1669 0.1648 0.1745 0.2066 0.2183 RANDOM 28.12
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] -0.4 0.53 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.856 r_dihedral_angle_4_deg 15.326 r_dihedral_angle_3_deg 15.209 r_dihedral_angle_1_deg 6.191 r_mcangle_it 2.68 r_angle_refined_deg 2.613 r_mcbond_it 1.835 r_mcbond_other 1.82 r_angle_other_deg 1.246 r_chiral_restr 0.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.856 r_dihedral_angle_4_deg 15.326 r_dihedral_angle_3_deg 15.209 r_dihedral_angle_1_deg 6.191 r_mcangle_it 2.68 r_angle_refined_deg 2.613 r_mcbond_it 1.835 r_mcbond_other 1.82 r_angle_other_deg 1.246 r_chiral_restr 0.163 r_bond_refined_d 0.03 r_gen_planes_refined 0.015 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1214 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 9
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing