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Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XQF PDB Entry 1XQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 28% PEG 400, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.22 61.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.175 α = 90 b = 108.175 β = 90 c = 84.663 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 MARMOSAIC 225 mm CCD 2006-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97934 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 2.2 20 99.6 0.07 15.41 28604 -3
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) 2.2 2.3 100 0.57 2.52
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 (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 PDB Entry 1XQF 2.2 15 27078 1447 99.73 0.20555 0.20555 0.2042 0.2527 0.23074 0.2686 RANDOM 30.101
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] 1.84 0.92 1.84 -2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.969 r_dihedral_angle_3_deg 14.764 r_dihedral_angle_4_deg 9.861 r_scangle_it 6.123 r_dihedral_angle_1_deg 5.627 r_scbond_it 5.04 r_mcangle_it 2.98 r_mcbond_it 1.977 r_angle_refined_deg 1.279 r_xyhbond_nbd_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.969 r_dihedral_angle_3_deg 14.764 r_dihedral_angle_4_deg 9.861 r_scangle_it 6.123 r_dihedral_angle_1_deg 5.627 r_scbond_it 5.04 r_mcangle_it 2.98 r_mcbond_it 1.977 r_angle_refined_deg 1.279 r_xyhbond_nbd_refined 0.317 r_nbtor_refined 0.316 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.128 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2641 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling MOLREP phasing