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Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with cyclic AMP (cAMP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293.15 Protein solution containing 19 mg/ml SbtB in 50 mM Tris.HCl (pH 8.0), 250 mM NaCl, 2mM cAMP mixed 1:1 with reservoir solution of Molecular Dimensions Morpheus screen condition G2
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.386 α = 90 b = 64.386 β = 90 c = 81.459 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.75 32.89 99.9 0.045 0.999 22.14 7.16 38069
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.86 99.7 0.961 0.815 2.13 7.04
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5O3P 1.75 32.89 36167 1901 99.93 0.17094 0.16976 0.19296 0.2141 RANDOM 40.159
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] 0.39 0.19 0.39 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_4_deg 34.522 r_dihedral_angle_3_deg 14.659 r_long_range_B_other 7.378 r_long_range_B_refined 7.376 r_dihedral_angle_1_deg 6.057 r_scangle_other 4.797 r_scbond_it 3.276 r_scbond_other 3.264 r_mcangle_it 3.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_4_deg 34.522 r_dihedral_angle_3_deg 14.659 r_long_range_B_other 7.378 r_long_range_B_refined 7.376 r_dihedral_angle_1_deg 6.057 r_scangle_other 4.797 r_scbond_it 3.276 r_scbond_other 3.264 r_mcangle_it 3.107 r_mcangle_other 3.106 r_mcbond_it 2.299 r_mcbond_other 2.299 r_angle_refined_deg 2.13 r_angle_other_deg 0.924 r_chiral_restr 0.129 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2245 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing