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Crystal structure of the e. coli ammonia channel AMTB complexed with the signal transduction protein GLNK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U7G PDB ENTRY 1U7G and PDB ENTRY 2GNK experimental model PDB 2GNK PDB ENTRY 1U7G and PDB ENTRY 2GNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20% PEG 550MME, 0.12M TRIS(HYDROXYMETHYL)AMINOMETHANE, 2mM ADENOSINE-5'-TRIPHOSPHATE, 25mM AMONIUM SULFATE, 0.04M B-OCTYLGLUCOSIDE, 2mM DITHIOTHREITOL, 0.05M SODIUM CHLORIDE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.28 62.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.032 α = 90 b = 102.032 β = 90 c = 363.849 γ = 120
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 4 SI(111) 2006-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1159 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.962 43.07 98.9 0.083 41.2 7.2 53722 52357 2 32.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.962 2.03 93.4 0.611 2.1 4.2 4864
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 1U7G and PDB ENTRY 2GNK 1.962 43.07 1 48839 48839 2562 97.47 0.16435 0.16248 0.1727 0.19838 0.2062 RANDOM 30.533
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] 0.12 0.06 0.12 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.139 r_dihedral_angle_4_deg 16.037 r_dihedral_angle_3_deg 13.042 r_scangle_it 5.74 r_dihedral_angle_1_deg 5.505 r_mcangle_it 4.879 r_mcbond_it 4.458 r_scbond_it 4.359 r_angle_other_deg 1.49 r_angle_refined_deg 1.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.139 r_dihedral_angle_4_deg 16.037 r_dihedral_angle_3_deg 13.042 r_scangle_it 5.74 r_dihedral_angle_1_deg 5.505 r_mcangle_it 4.879 r_mcbond_it 4.458 r_scbond_it 4.359 r_angle_other_deg 1.49 r_angle_refined_deg 1.484 r_mcbond_other 1.261 r_symmetry_vdw_other 0.236 r_chiral_restr 0.224 r_nbd_refined 0.207 r_nbtor_refined 0.185 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.169 r_symmetry_vdw_refined 0.154 r_nbtor_other 0.086 r_xyhbond_nbd_other 0.017 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3838 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing