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Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J9C PDB ENTRY 2J9C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.17 43.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.6 α = 90 b = 107.03 β = 90 c = 134.34 γ = 90
Symmetry Space Group P 21 21 21
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 CCD 2004-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 20 99 0.16 11.3 4.6 80980 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 98.8 0.53 3.06 4.6
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2J9C 2.1 19.78 76930 4050 100 0.21 0.207 0.265 RANDOM 30.31
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] 0.77 0.58 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.328 r_dihedral_angle_4_deg 17.293 r_dihedral_angle_3_deg 17.209 r_dihedral_angle_1_deg 6.954 r_scangle_it 4.835 r_scbond_it 3.477 r_mcangle_it 2.673 r_mcbond_it 2.279 r_angle_refined_deg 1.446 r_angle_other_deg 0.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.328 r_dihedral_angle_4_deg 17.293 r_dihedral_angle_3_deg 17.209 r_dihedral_angle_1_deg 6.954 r_scangle_it 4.835 r_scbond_it 3.477 r_mcangle_it 2.673 r_mcbond_it 2.279 r_angle_refined_deg 1.446 r_angle_other_deg 0.944 r_symmetry_vdw_other 0.304 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.212 r_nbd_other 0.207 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.164 r_symmetry_hbond_refined 0.132 r_nbtor_other 0.085 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9994 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing