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Crystal structure of the GGDEF domain of PA1120 (YfiN or TpbB) from Pseudomonas aeruginosa at 2.7 Ang.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WB4 PDB ENTRY 2WB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 294 300nl+300nl of 3.7 mg/ml protein solution (100 mM NaCl, 10 mM Tris pH=8.0, 2% glycerol) and 0.1 M Sodium Citrate dehydrate pH 5.6, 35% v/v tert-butanol., VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.18 43.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.351 α = 90 b = 70.351 β = 90 c = 106.866 γ = 120
Symmetry Space Group P 65 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 ADSC QUANTUM 210 2012-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1
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 2.78 40 99.6 0.095 0.083 31.11 13.7 4359 4343 3 3 57.9
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 2.78 2.94 0.607 0.685 3.3 9.77 666
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2WB4 2.78 40 4095 217 99.7 0.27841 0.27833 0.2747 0.27978 0.2826 RANDOM 48.086
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] -2.11 -1.06 -2.11 3.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.269 r_dihedral_angle_3_deg 15.058 r_dihedral_angle_4_deg 11.077 r_dihedral_angle_1_deg 3.002 r_angle_refined_deg 0.46 r_chiral_restr 0.031 r_bond_refined_d 0.001 r_gen_planes_refined 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1230 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 11
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling