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Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with activating cofactor Mg++
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 10 % of amino acid mixture (200 mM of each of Sodium-L-glutamate, M DL-alanine, Glycin and L-Lysine HCl, 0.2 M DL-Serin), 100 mM MES/Imidazole pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.85 α = 90 b = 109.547 β = 99.39 c = 81.75 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 PIXEL DECTRIS PILATUS 2M 2012-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
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 2.4 109.55 99.63 0.053 14.5822 3.4 43912 -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 2.4 2.53 99.79 0.45 1.76 3.31 6344
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 4KIE 2.4 30 43884 2209 99.58 0.1902 0.1886 0.1912 0.222 0.2235 50.282
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] -1.95 -1.56 -0.18 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.807 r_dihedral_angle_4_deg 18.817 r_dihedral_angle_3_deg 17.533 r_dihedral_angle_1_deg 5.403 r_angle_refined_deg 1.423 r_angle_other_deg 1.192 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.807 r_dihedral_angle_4_deg 18.817 r_dihedral_angle_3_deg 17.533 r_dihedral_angle_1_deg 5.403 r_angle_refined_deg 1.423 r_angle_other_deg 1.192 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7881 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing