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The mechanism of ammonia transport based on the crystal structure of AmtB of E. coli.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XQF The same structure in the absence of ammonium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 PEG 550, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.9 68.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.632 α = 90 b = 116.632 β = 90 c = 130.543 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 MARRESEARCH 2004-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9797 SLS X06SA
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 2.1 79.06 99.7 0.073 13.6 5.8 38583 -3 44.4
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 2.1 2.15 99.9 0.7 2.5 5.7 2677
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 The same structure in the absence of ammonium 2.1 60 36648 36648 1935 99.72 0.16051 0.16051 0.15912 0.1863 0.18603 0.2107 RANDOM 42.765
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] 1.58 0.79 1.58 -2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.451 r_dihedral_angle_4_deg 25.424 r_dihedral_angle_3_deg 13.518 r_scangle_it 6.173 r_dihedral_angle_1_deg 5.267 r_scbond_it 4.726 r_mcangle_it 3.147 r_mcbond_it 2.205 r_angle_refined_deg 1.236 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.451 r_dihedral_angle_4_deg 25.424 r_dihedral_angle_3_deg 13.518 r_scangle_it 6.173 r_dihedral_angle_1_deg 5.267 r_scbond_it 4.726 r_mcangle_it 3.147 r_mcbond_it 2.205 r_angle_refined_deg 1.236 r_nbtor_refined 0.307 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.187 r_symmetry_hbond_refined 0.128 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2660 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling AMoRE phasing