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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 26% PEG 550, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.35 63.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.23 α = 90 b = 110.23 β = 90 c = 84.642 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 2006-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9998 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 20 97.5 0.05 17.74 38571 -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) 1 2 2.1 99.7 0.47 3.44
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 15 36605 1936 97.68 0.18285 0.18285 0.18147 0.2471 0.20974 0.2706 RANDOM 27.21
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] 1.04 0.52 1.04 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.468 r_dihedral_angle_3_deg 12.621 r_dihedral_angle_4_deg 10.505 r_scangle_it 6.421 r_scbond_it 5.074 r_dihedral_angle_1_deg 4.744 r_mcangle_it 3.043 r_mcbond_it 2.304 r_angle_refined_deg 0.999 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.468 r_dihedral_angle_3_deg 12.621 r_dihedral_angle_4_deg 10.505 r_scangle_it 6.421 r_scbond_it 5.074 r_dihedral_angle_1_deg 4.744 r_mcangle_it 3.043 r_mcbond_it 2.304 r_angle_refined_deg 0.999 r_nbtor_refined 0.3 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.149 r_symmetry_hbond_refined 0.139 r_xyhbond_nbd_refined 0.098 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2636 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling MOLREP phasing