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Structure of the hybrid domain (GGDEF-EAL) of PA0575 from Pseudomonas aeruginosa PAO1 at 2.8 Ang. with GTP and Ca2+ bound to the active site of the GGDEF domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RNJ 4RNJ, 4IOB experimental model PDB 4IOB 4RNJ, 4IOB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 Protein solution: 3 mg/ml in 20 mM Tris pH 7.6, 150 mM, CaCl2 2,5mM, GTP 0.32 mM
mixing volumes 1 microL (1:1)
Reservoir: PEG 4K 2%, CaCl2 0,01M, KCl 0,05 M, sodium cacodilato pH 6 0,05M
Cryo-protection:PEG 4K raised to 3%, addition of 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.88 57.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.307 α = 90 b = 133.931 β = 90 c = 69.141 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX SX-165mm 2016-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.894 BESSY 14.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.8 48.1 99.9 0.147 0.998 14.6 8.1 28700 55.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 99.7 1.342 0.74 8.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT 4RNJ, 4IOB 2.8 48.1 27257 1388 99.79 0.2452 0.2436 0.2466 0.2773 0.2737 RANDOM 61.268
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] -4.84 2.6 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.066 r_dihedral_angle_4_deg 17.128 r_dihedral_angle_3_deg 16.47 r_dihedral_angle_1_deg 3.996 r_mcangle_it 2.202 r_mcbond_it 1.226 r_mcbond_other 1.226 r_angle_refined_deg 0.741 r_angle_other_deg 0.543 r_chiral_restr 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.066 r_dihedral_angle_4_deg 17.128 r_dihedral_angle_3_deg 16.47 r_dihedral_angle_1_deg 3.996 r_mcangle_it 2.202 r_mcbond_it 1.226 r_mcbond_other 1.226 r_angle_refined_deg 0.741 r_angle_other_deg 0.543 r_chiral_restr 0.04 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6411 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 69
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling