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Crystal Structure of the G20A/C92U mutant c-di-GMP riboswith bound to c-di-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IRW PDB ENTRY 3IRW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 298 25% PEG 550 MME, 5 mM MgSO4, 50 mM MES, pH 6.0, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.05 39.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.87 α = 90 b = 45.898 β = 95.48 c = 75.696 γ = 90
Symmetry Space Group P 1 21 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 315 PT-COATED MIRROR 2009-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
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 3.2 80 90 0.197 5.6 3.2 4829
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) 3.2 3.3 63.6 0.333 2.2 2.2
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 PDB ENTRY 3IRW 3.2 48.65 4829 244 90.3 0.19 0.187 0.2002 0.26 0.2697 RANDOM 41.09
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] 2.4 3.54 -4.9 3.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.579 r_angle_refined_deg 1.112 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.579 r_angle_refined_deg 1.112 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 734 Nucleic Acid Atoms 1960 Solvent Atoms 16 Heterogen Atoms 45
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling