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Crystal structure of human phosphatase PTEN in its reduced state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES pH 6.5, 1.25 M L-tartrate, 7.5% glycerol
Crystal Properties Matthews coefficient Solvent content 3.16 61.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.17 α = 90 b = 207.39 β = 90 c = 87.78 γ = 90
Symmetry Space Group C 2 2 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 PIXEL PSI PILATUS 6M 2014-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00001 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.2 46.364 99.9 0.15 0.156 13.96 13.48 95899 -3 53.173
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 99.9 2.637 2.739 1.17
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 1d5r 2.2 46.36 91156 4742 99.62 0.1934 0.192 0.1905 0.2207 0.2194 RANDOM 58.472
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] -34.76 -31.32 66.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.007 r_dihedral_angle_4_deg 20.334 r_dihedral_angle_3_deg 17.737 r_dihedral_angle_1_deg 11.945 r_mcangle_it 4.658 r_mcbond_it 2.961 r_mcbond_other 2.961 r_angle_refined_deg 1.567 r_angle_other_deg 1.461 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.007 r_dihedral_angle_4_deg 20.334 r_dihedral_angle_3_deg 17.737 r_dihedral_angle_1_deg 11.945 r_mcangle_it 4.658 r_mcbond_it 2.961 r_mcbond_other 2.961 r_angle_refined_deg 1.567 r_angle_other_deg 1.461 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10338 Nucleic Acid Atoms Solvent Atoms 890 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction