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Crystal Structure of Protein Phosphatase-1 Bound to the natural toxin inhibitor Tautomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E7A PDB entry 3E7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 298 0.1M Tris, 30% PEG 6K, 1M Lithium Sulfate, pH 8.0, under paraffin oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.76 α = 90 b = 78.519 β = 90 c = 130.764 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 93 CCD ADSC QUANTUM 210 OXFORD DANFYSIK TOROIDAL FOCUSING MIRROR. 2008-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.7 50 99.2 0.046 5.7 74099 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 93.3 0.511 2.5 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 3E7A 1.7 19.63 74713 70860 3750 99.22 0.15408 0.15294 0.1587 0.17521 0.1778 RANDOM 20.298
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 0.09 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.934 r_dihedral_angle_4_deg 14.897 r_dihedral_angle_3_deg 11.312 r_dihedral_angle_1_deg 6.55 r_scangle_it 5.036 r_scbond_it 3.65 r_mcangle_it 2.284 r_angle_refined_deg 1.571 r_mcbond_it 1.391 r_angle_other_deg 1.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.934 r_dihedral_angle_4_deg 14.897 r_dihedral_angle_3_deg 11.312 r_dihedral_angle_1_deg 6.55 r_scangle_it 5.036 r_scbond_it 3.65 r_mcangle_it 2.284 r_angle_refined_deg 1.571 r_mcbond_it 1.391 r_angle_other_deg 1.096 r_mcbond_other 0.409 r_nbd_refined 0.202 r_nbd_other 0.202 r_symmetry_vdw_other 0.2 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.162 r_symmetry_vdw_refined 0.147 r_chiral_restr 0.137 r_metal_ion_refined 0.118 r_nbtor_other 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4630 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 140
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction