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Controlling the storage of nitrogen as arginine: the complex of PII and acetylglutamate kinase from Synechococcus elongatus PCC 7942
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JJ4 PDB ENTRY 2JJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1 M TRIS-HCL PH 8.5, 0.15 M SODIUM ACETATE, 20% (WT/VOL) POLYETHYLENE GLYCOL 4K, 20 MM ACETYLGLUTAMATE.
Crystal Properties Matthews coefficient Solvent content 2.3 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.379 α = 90 b = 161.027 β = 106.53 c = 91.562 γ = 90
Symmetry Space Group P 1 21 1
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 RD COATED FLAT MIRROR AND RD COATED TOROIDAL MIRROR 2006-03-21 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARRESEARCH M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3 2 SYNCHROTRON ESRF BEAMLINE BM16 ESRF BM16
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 2.75 87.71 100 0.08 6.9 5.1 65178 2 61.3
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 2.75 2.9 100 0.37 2 5.2
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 2JJ4 2.75 50 61827 3297 100 0.202 0.2 0.236 RANDOM 38.31
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] -0.2 0.09 -0.25 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.972 r_dihedral_angle_4_deg 22.311 r_dihedral_angle_3_deg 18.875 r_dihedral_angle_1_deg 6.396 r_scangle_it 2.573 r_scbond_it 1.419 r_angle_refined_deg 1.375 r_mcangle_it 0.796 r_mcbond_it 0.394 r_symmetry_hbond_refined 0.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.972 r_dihedral_angle_4_deg 22.311 r_dihedral_angle_3_deg 18.875 r_dihedral_angle_1_deg 6.396 r_scangle_it 2.573 r_scbond_it 1.419 r_angle_refined_deg 1.375 r_mcangle_it 0.796 r_mcbond_it 0.394 r_symmetry_hbond_refined 0.389 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 17828 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing