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Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with ATP and ADP resulting from long ATP soak
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, SITTING DROP 294 0.2 M SODIUM ACETATE, 0.1 M HEPES PH 7.5, 20 % (W/V) PEG3000
Crystal Properties Matthews coefficient Solvent content 2.11 41.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.802 α = 90 b = 60.802 β = 90 c = 78.435 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 2016-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 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 2.4 31.45 99.8 0.058 0.999 20.8 7.23 12684
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 2.4 2.54 98.8 0.784 0.863
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5O3P 2.4 31.45 12048 636 99.62 0.18756 0.18615 0.1926 0.21331 0.2146 RANDOM 66.327
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] 0.88 0.44 0.88 -2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.86 r_dihedral_angle_4_deg 19.371 r_dihedral_angle_3_deg 16.255 r_long_range_B_refined 9.44 r_long_range_B_other 9.44 r_dihedral_angle_1_deg 7.055 r_scangle_other 6.653 r_scbond_it 4.585 r_scbond_other 4.585 r_mcangle_it 4.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.86 r_dihedral_angle_4_deg 19.371 r_dihedral_angle_3_deg 16.255 r_long_range_B_refined 9.44 r_long_range_B_other 9.44 r_dihedral_angle_1_deg 7.055 r_scangle_other 6.653 r_scbond_it 4.585 r_scbond_other 4.585 r_mcangle_it 4.353 r_mcangle_other 4.352 r_mcbond_other 2.981 r_mcbond_it 2.98 r_angle_refined_deg 2.084 r_angle_other_deg 1.136 r_chiral_restr 0.083 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.006 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 2242 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling