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Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 0.1 M Na-Acetate pH 4.6 and 40% PEG200, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.626 α = 90 b = 87.818 β = 90 c = 94.723 γ = 90
Symmetry Space Group I 2 2 2
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 MARMOSAIC 225 mm CCD 2011-03-06 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 1.7 47.36 99.8 0.055 15.722 6.14 34026 -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 1.7 1.79 100 0.44 1.66 6.14 4904
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 2R6O 1.7 30 34019 1726 99.73 0.1665 0.1654 0.1764 0.1853 0.1964 27.497
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] -0.57 -0.71 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.243 r_dihedral_angle_4_deg 25.512 r_dihedral_angle_3_deg 13.677 r_dihedral_angle_1_deg 5.825 r_angle_refined_deg 1.445 r_angle_other_deg 0.795 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.243 r_dihedral_angle_4_deg 25.512 r_dihedral_angle_3_deg 13.677 r_dihedral_angle_1_deg 5.825 r_angle_refined_deg 1.445 r_angle_other_deg 0.795 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2054 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing