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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 3.29 62.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.329 α = 90 b = 109.329 β = 90 c = 84.821 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 2007-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9772 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 2.3 20 98.7 0.05 17.2 25706 -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) 2.3 2.4 97.6 0.48 2.48
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 1XQF 2.3 15 36372 24136 1300 99.36 0.18788 0.18788 0.18507 0.24203 0.2563 RANDOM 35.155
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] 2.06 1.03 2.06 -3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.011 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_4_deg 9.378 r_scangle_it 6.071 r_dihedral_angle_1_deg 5.214 r_scbond_it 5.107 r_mcangle_it 2.975 r_mcbond_it 1.906 r_angle_refined_deg 1.19 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.011 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_4_deg 9.378 r_scangle_it 6.071 r_dihedral_angle_1_deg 5.214 r_scbond_it 5.107 r_mcangle_it 2.975 r_mcbond_it 1.906 r_angle_refined_deg 1.19 r_nbtor_refined 0.315 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.225 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2648 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling MOLREP phasing