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Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1), the PP1 binding and PDZ domains of Spinophilin and the small natural molecular toxin Nodularin-R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 277 0.1M MES, 15% PEG 550 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.42 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.409 α = 90 b = 84.426 β = 93.58 c = 109.314 γ = 90
Symmetry Space Group C 1 2 1
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 DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL HORIZONTAL FOCUSING 2008-07-19 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 2 40 98.1 0.066 3.6 70101 26.55
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 2 2.07 82.5 0.281 3.45 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 2 40 69145 66573 3528 96.3 0.195 0.192 0.1911 0.235 0.2322 RANDOM 30.11
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] -0.35 1.11 0.7 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.581 r_dihedral_angle_4_deg 15.012 r_dihedral_angle_3_deg 14.136 r_dihedral_angle_1_deg 6.224 r_scangle_it 3.222 r_scbond_it 2.16 r_angle_refined_deg 1.544 r_mcangle_it 1.243 r_mcbond_it 0.804 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.581 r_dihedral_angle_4_deg 15.012 r_dihedral_angle_3_deg 14.136 r_dihedral_angle_1_deg 6.224 r_scangle_it 3.222 r_scbond_it 2.16 r_angle_refined_deg 1.544 r_mcangle_it 1.243 r_mcbond_it 0.804 r_nbtor_refined 0.31 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6436 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 28
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing