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Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in Apo state, trigonal crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.2 293.15 Protein solution containing 19 mg/ml SbtB in 50 mM Tris.HCl (pH 8.0), 250 mM NaCl mixed 1:1 with reservoir solution composed of 0.1 M phosphate-citrate pH 4.2, and 40 % (w/v) PEG300.
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.351 α = 90 b = 64.351 β = 90 c = 82.52 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 2015-09-21 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 33.16 99.7 0.051 0.999 18.62 7.2 38551
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 1.85 97.9 0.796 0.777 2.07 7.14
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 MOLECULAR REPLACEMENT THROUGHOUT 3DFE 1.75 33.16 36652 1898 99.65 0.16525 0.16374 0.173 0.19377 0.1974 RANDOM 40.374
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] 0.43 0.22 0.43 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.962 r_dihedral_angle_4_deg 28.999 r_dihedral_angle_3_deg 13.517 r_long_range_B_refined 7.837 r_long_range_B_other 7.794 r_dihedral_angle_1_deg 6.19 r_scangle_other 5.397 r_scbond_it 3.772 r_scbond_other 3.772 r_mcangle_it 3.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.962 r_dihedral_angle_4_deg 28.999 r_dihedral_angle_3_deg 13.517 r_long_range_B_refined 7.837 r_long_range_B_other 7.794 r_dihedral_angle_1_deg 6.19 r_scangle_other 5.397 r_scbond_it 3.772 r_scbond_other 3.772 r_mcangle_it 3.239 r_mcangle_other 3.238 r_mcbond_it 2.469 r_mcbond_other 2.455 r_angle_refined_deg 1.98 r_angle_other_deg 0.922 r_chiral_restr 0.137 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 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 2256 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing