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Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H0L PDB entry 2H0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1:1 ratio of Protein solution (6-9mg/ml GatCAB,10mM HEPES, 50uM Zn acetate,10mM Gln, 0.6mM ATP) mix with well solution (10-12% PEG3350, 10mM Mg formate), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.248 α = 90.01 b = 129.856 β = 89.96 c = 155.069 γ = 90.11
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 300 mm CCD 2005-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0274 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.8 39.4 98 0.061 0.061 11.5 2 241473 241473
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 96.8 0.478 0.478 1.6 1.9
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 (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 2H0L 2.8 39.37 241468 229209 12256 98 0.25623 0.25364 0.26 0.3054 0.263 RANDOM 61.581
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] -4.1 0.42 0.33 8.81 1.49 -4.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.852 r_dihedral_angle_4_deg 20.316 r_dihedral_angle_3_deg 20.057 r_dihedral_angle_1_deg 7.01 r_angle_refined_deg 1.491 r_nbtor_refined 0.316 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.239 r_symmetry_hbond_refined 0.233 r_xyhbond_nbd_refined 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.852 r_dihedral_angle_4_deg 20.316 r_dihedral_angle_3_deg 20.057 r_dihedral_angle_1_deg 7.01 r_angle_refined_deg 1.491 r_nbtor_refined 0.316 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.239 r_symmetry_hbond_refined 0.233 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.104 r_bond_refined_d 0.013 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 62848 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 87
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling