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Gbeta1 stabilization by in vitro evolution and computational design
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PGA PDB ENTRY 1PGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 50mM Na acetate, pH 5.0, 17 mg/ml protein mixed with equal volume of 2.3M ammonium suphate, 0.1M sodium acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.104 α = 90 b = 52.104 β = 90 c = 22.765 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MAR CCD 165 mm mirrors 2006-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.34 50 94.6 0.053 18 7.1 14227 13293
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.39 56.4 0.365 0.365 3.1 770
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 (All) 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 1PGA 1.35 19 12697 12044 635 92.35 0.162 0.16 0.158 0.1628 0.195 0.2064 RANDOM 20.64
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] 0.27 0.27 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.024 r_sphericity_free 13.886 r_dihedral_angle_3_deg 11.273 r_scangle_it 8.73 r_sphericity_bonded 6.953 r_scbond_it 6.546 r_dihedral_angle_1_deg 5.646 r_mcangle_it 4.937 r_mcbond_it 4.339 r_rigid_bond_restr 3.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.024 r_sphericity_free 13.886 r_dihedral_angle_3_deg 11.273 r_scangle_it 8.73 r_sphericity_bonded 6.953 r_scbond_it 6.546 r_dihedral_angle_1_deg 5.646 r_mcangle_it 4.937 r_mcbond_it 4.339 r_rigid_bond_restr 3.274 r_angle_other_deg 2.462 r_angle_refined_deg 2.434 r_mcbond_other 1.999 r_symmetry_vdw_refined 0.57 r_nbd_refined 0.224 r_nbtor_refined 0.194 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.168 r_nbd_other 0.166 r_symmetry_vdw_other 0.132 r_chiral_restr 0.122 r_nbtor_other 0.106 r_bond_refined_d 0.026 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 444 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection