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Crystal Structure of Bcy1, the Yeast Regulatory Subunit of PKA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RGS 1RGS A-domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 15% polyethylene glycol 3350, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.34 47.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.425 α = 90 b = 45.042 β = 92.51 c = 39.103 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 200 CCD ADSC QUANTUM 315 2008-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0000 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 50 91.4 0.058 0.051 23.2 3.4 12845 12845 2 2
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) 2.2 2.28 55.5 0.234 0.227 3.8 1.9 713
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RGS A-domain 2.21 50 2 12845 11232 565 91.4 0.2 0.2 0.2004 0.263 RANDOM 44.627
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] 2.36 -0.37 -0.7 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.369 r_dihedral_angle_4_deg 21.236 r_dihedral_angle_3_deg 19.809 r_dihedral_angle_1_deg 7.885 r_scangle_it 4.601 r_scbond_it 3.274 r_angle_refined_deg 2.2 r_mcangle_it 2.165 r_mcbond_it 1.287 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.369 r_dihedral_angle_4_deg 21.236 r_dihedral_angle_3_deg 19.809 r_dihedral_angle_1_deg 7.885 r_scangle_it 4.601 r_scbond_it 3.274 r_angle_refined_deg 2.2 r_mcangle_it 2.165 r_mcbond_it 1.287 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.241 r_symmetry_hbond_refined 0.225 r_xyhbond_nbd_refined 0.214 r_chiral_restr 0.162 r_bond_refined_d 0.025 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1820 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 44
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling