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The crystal structure of syn_CdgR-(c-di-GMP) from Synechocystis sp. PCC 6803
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 21% PEG 3350, 0.2 M sodium chloride, 0.1 M Bis-Tris pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.94 58.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.327 α = 90 b = 55.978 β = 111.97 c = 91.692 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 100 CCD ADSC QUANTUM 315r 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.35 50 99.4 0.978 27.43 6.2 18257
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 95.9 0.892 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.38 47.48 15940 1790 95.98 0.23076 0.22445 0.2424 0.28568 0.2833 RANDOM 39.799
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] -0.24 -0.08 0.48 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.878 r_long_range_B_refined 11.784 r_long_range_B_other 11.753 r_dihedral_angle_1_deg 8.539 r_mcangle_it 7.304 r_mcangle_other 7.301 r_dihedral_angle_2_deg 7.226 r_scangle_other 7.118 r_scbond_other 4.54 r_scbond_it 4.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.878 r_long_range_B_refined 11.784 r_long_range_B_other 11.753 r_dihedral_angle_1_deg 8.539 r_mcangle_it 7.304 r_mcangle_other 7.301 r_dihedral_angle_2_deg 7.226 r_scangle_other 7.118 r_scbond_other 4.54 r_scbond_it 4.537 r_mcbond_it 4.456 r_mcbond_other 4.451 r_angle_refined_deg 1.707 r_angle_other_deg 0.521 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2179 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 92
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling PHENIX phasing Coot model building