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Structure of cAMP-dependent protein kinase complexed with A-443654
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDS PDB ENTRY 1YDS
Crystallization Crystal Properties Matthews coefficient Solvent content 2.36 47.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.538 α = 90 b = 75.061 β = 90 c = 80.133 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 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 2 36 99 0.06 9.2 3.3 28286
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 95 0.4 1.8 2.6
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1YDS 2 36.27 28286 1512 98.7 0.211 0.208 0.272 RANDOM 28.46
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] 1.29 -0.29 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.608 r_dihedral_angle_4_deg 21.553 r_dihedral_angle_3_deg 15.399 r_dihedral_angle_1_deg 5.778 r_angle_refined_deg 1.334 r_angle_other_deg 0.875 r_symmetry_vdw_other 0.276 r_nbd_refined 0.203 r_nbd_other 0.19 r_nbtor_refined 0.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.608 r_dihedral_angle_4_deg 21.553 r_dihedral_angle_3_deg 15.399 r_dihedral_angle_1_deg 5.778 r_angle_refined_deg 1.334 r_angle_other_deg 0.875 r_symmetry_vdw_other 0.276 r_nbd_refined 0.203 r_nbd_other 0.19 r_nbtor_refined 0.185 r_symmetry_vdw_refined 0.134 r_xyhbond_nbd_refined 0.124 r_scangle_it 0.095 r_nbtor_other 0.084 r_chiral_restr 0.078 r_symmetry_hbond_refined 0.077 r_mcangle_it 0.077 r_scbond_it 0.075 r_mcbond_it 0.058 r_bond_refined_d 0.013 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_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2947 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement