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Crystal structure of putative diguanylate cyclase/phosphodiesterase from Listaria monocytigenes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 293 0.2 M Ca acetate, 0.1 M Na cacodilate, 9% PEG 8K, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 48.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.766 α = 90 b = 92.04 β = 90 c = 96.21 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 315 MIRROR 2008-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9786 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 50 93.7 0.091 0.091 21.885 6.5 34443 34443 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 88 0.513 0.513 2.8 5.9 1520
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 (All) 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 50 34327 34327 1714 93.86 0.187 0.187 0.185 0.1959 0.239 0.2471 RANDOM 13.14
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] 0.11 1.44 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.118 r_dihedral_angle_4_deg 15.007 r_dihedral_angle_3_deg 13.975 r_dihedral_angle_1_deg 6.303 r_scangle_it 4.135 r_scbond_it 2.698 r_angle_refined_deg 1.75 r_mcangle_it 1.617 r_angle_other_deg 0.999 r_mcbond_it 0.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.118 r_dihedral_angle_4_deg 15.007 r_dihedral_angle_3_deg 13.975 r_dihedral_angle_1_deg 6.303 r_scangle_it 4.135 r_scbond_it 2.698 r_angle_refined_deg 1.75 r_mcangle_it 1.617 r_angle_other_deg 0.999 r_mcbond_it 0.959 r_mcbond_other 0.296 r_chiral_restr 0.104 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3771 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 18
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing MLPHARE phasing DM model building SHELXD phasing RESOLVE model building ARP/wARP model building REFMAC refinement Coot model building HKL-3000 data reduction HKL-2000 data scaling DM phasing RESOLVE phasing