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Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase in complex with its feed- back inhibitor L-arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZZF PDB ENTRY 3ZZF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 PROTEIN WAS CRYSTALLIZED IN 50 MM NA-ACETATE, PH 4.6, 0.2 M NA-MALONATE AND 2% PEG 8000,, CONTAINING 24MM N-ACETYLGLUTAMATE (NAG); 24 HOURS BEFORE FREEZING ARGININE 0.2 M WAS ADDED TO CRYSTALLIZATION DROP. 20% GLYCEROL WAS USED AS CRYOPROTECTOR
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.489 α = 90 b = 99.596 β = 90 c = 189.238 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 2010-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 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 2.1 20 99.6 0.13 3.8 4.8 77012 1.9 19.8
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 2.21 99.6 0.37 1.9 4.7
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 3ZZF 2.1 20 72907 3860 99.27 0.18211 0.18037 0.1939 0.21544 0.2304 RANDOM 22.225
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] -0.32 0.26 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.555 r_dihedral_angle_4_deg 17.913 r_dihedral_angle_3_deg 13.565 r_dihedral_angle_1_deg 5.699 r_scangle_it 2.003 r_scbond_it 1.143 r_angle_refined_deg 1.019 r_angle_other_deg 0.801 r_mcangle_it 0.649 r_mcbond_it 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.555 r_dihedral_angle_4_deg 17.913 r_dihedral_angle_3_deg 13.565 r_dihedral_angle_1_deg 5.699 r_scangle_it 2.003 r_scbond_it 1.143 r_angle_refined_deg 1.019 r_angle_other_deg 0.801 r_mcangle_it 0.649 r_mcbond_it 0.326 r_mcbond_other 0.061 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_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 8953 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 276
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing