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Crystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic di-gmp
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.2 M MAGNESIUM CHLORIDE, 25% PEG3350, 0.1M BIS-TRIS, 2.5MM CYCLIC DI-GMP, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 42.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.56 α = 90 b = 63.201 β = 90 c = 173.987 γ = 90
Symmetry Space Group P 21 21 21
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 210r 2009-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97940 APS 19-BM
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 2.35 50 99.9 0.1 34.6 6.9 24452 24433 -3
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) 1 2.35 2.37 99.9 0.459 5.19 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 2.35 39.955 24286 23047 1239 99.38 0.18757 0.18403 0.25363 0.2513 RANDOM 30.76
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] 4.92 -2.1 -2.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.672 r_dihedral_angle_4_deg 17.546 r_dihedral_angle_3_deg 17.082 r_dihedral_angle_1_deg 5.58 r_scangle_it 4.651 r_scbond_it 2.902 r_mcangle_it 1.766 r_angle_refined_deg 1.537 r_rigid_bond_restr 1.502 r_mcbond_it 0.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.672 r_dihedral_angle_4_deg 17.546 r_dihedral_angle_3_deg 17.082 r_dihedral_angle_1_deg 5.58 r_scangle_it 4.651 r_scbond_it 2.902 r_mcangle_it 1.766 r_angle_refined_deg 1.537 r_rigid_bond_restr 1.502 r_mcbond_it 0.953 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_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_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4000 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 97
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM model building RESOLVE model building Coot model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing