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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 2GI3 PDB entries 2GI3 and 2G5H experimental model PDB 2G5H PDB entries 2GI3 and 2G5H
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 Asn, 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 54.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.482 α = 90.02 b = 131.012 β = 90 c = 154.668 γ = 89.91
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 MONOCHROMATOR: MIRRORS 2006-03-24 M MAD 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD MONOCHROMATOR: MIRRORS 2007-03-20 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0274,0.9804 APS 23-ID-D 2 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 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 2.3 40.5 91.5 0.06 0.06 11.5 1.9 405875 405875
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) 2.3 2.35 73.7 0.347 0.347 1.8 1.7
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 entries 2GI3 and 2G5H 2.3 40.5 405875 385553 20322 91.69 0.24169 0.24004 0.2512 0.2726 0.2754 RANDOM 50.929
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] -4.63 -0.01 -0.26 9.07 0.04 -4.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.072 r_dihedral_angle_3_deg 18.656 r_dihedral_angle_4_deg 17.933 r_dihedral_angle_1_deg 6.149 r_scangle_it 2.305 r_scbond_it 1.454 r_angle_refined_deg 1.396 r_mcangle_it 1.11 r_mcbond_it 0.672 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.072 r_dihedral_angle_3_deg 18.656 r_dihedral_angle_4_deg 17.933 r_dihedral_angle_1_deg 6.149 r_scangle_it 2.305 r_scbond_it 1.454 r_angle_refined_deg 1.396 r_mcangle_it 1.11 r_mcbond_it 0.672 r_nbtor_refined 0.309 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.215 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.166 r_metal_ion_refined 0.098 r_chiral_restr 0.094 r_bond_refined_d 0.012 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other 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 296
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling