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Crystal structure of a tetrameric acetylglutamate kinase from Saccharomyces cerevisiae complexed with its substrate N- acetylglutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZZI PDB ENTRY 3ZZI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION OF SURFACE EXPOSED LYSINES WITH ABC PREVIOUS TO CRYSTALLIZATION. 10 MG/ML PROTEIN IN 20MM HEPES PH7.5, 0.5 M NACL, 1MM MSH, AND SUPPLEMENTED WITH 40 MM NAG, WAS CRYSTALLIZED IN PRESENCE OF 0.2 M AMMONIUM CITRATE PH 7.0, 12 % PEG3350 AND 1.5 % PEG 6000 AS CRYSTALLIZATION SOLUTION, IN SITTING DROPS AT 4C. CRYOBUFFER SOLUTION WAS THAT OF CRYSTALLIZATION WITH PEG3350 ENRICHED TO 40%
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.883 α = 77.31 b = 103.269 β = 89.27 c = 111.313 γ = 70.43
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 MARRESEARCH 2011-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 3.25 108 96.2 0.07 9.6 1.9 57473 1.7
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 3.25 3.43 96.2 0.46 1.7 1.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3ZZI 3.25 108.36 54576 2896 96.17 0.195 0.19275 0.196 0.23757 0.2403 RANDOM 93.288
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] 0.73 -0.51 -0.96 -0.06 -0.46 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.71 r_dihedral_angle_4_deg 21.456 r_dihedral_angle_3_deg 20.955 r_dihedral_angle_1_deg 7.117 r_angle_other_deg 1.993 r_angle_refined_deg 1.76 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_bond_other_d 0.011 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.71 r_dihedral_angle_4_deg 21.456 r_dihedral_angle_3_deg 20.955 r_dihedral_angle_1_deg 7.117 r_angle_other_deg 1.993 r_angle_refined_deg 1.76 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_bond_other_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 26294 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing