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Crystal structure of human phosphatase PTEN treated with a bisperoxovanadium complex
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-tartrat, 7.5% glycerol
Crystal Properties Matthews coefficient Solvent content 3.15 60.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.06 α = 90 b = 206.9 β = 90 c = 87.67 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 1.77119 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 2.5 46.293 100 0.118 0.123 17.43 12.91 65393 -3 56.698
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 2.5 2.6 100 1.552 1.619 1.53
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 2.5 46.29 62095 3297 99.75 0.1767 0.1752 0.1757 0.2037 0.2037 RANDOM 59.842
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] -33.11 -30.39 63.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.762 r_dihedral_angle_4_deg 22.534 r_dihedral_angle_3_deg 18.237 r_dihedral_angle_1_deg 12.46 r_mcangle_it 5.666 r_mcbond_it 3.55 r_mcbond_other 3.549 r_angle_refined_deg 1.538 r_angle_other_deg 1.451 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.762 r_dihedral_angle_4_deg 22.534 r_dihedral_angle_3_deg 18.237 r_dihedral_angle_1_deg 12.46 r_mcangle_it 5.666 r_mcbond_it 3.55 r_mcbond_other 3.549 r_angle_refined_deg 1.538 r_angle_other_deg 1.451 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10310 Nucleic Acid Atoms Solvent Atoms 880 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction