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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 3H0L PDB entry 3H0L
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), crystal soaked in the mother liquor with 10mMAsn, 10mM Asp, 10mM ATP, 10mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.377 α = 89.89 b = 130.411 β = 90.21 c = 153.973 γ = 89.95
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 2007-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 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 3 49 91.2 0.112 0.112 5.8 1.7 232054 182013
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) 3 3.11 84.5 0.71 0.71 1.2 1.6
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 3H0L 3 48.97 190557 180942 9614 96.04 0.26515 0.26299 0.2578 0.30604 0.2975 RANDOM 60.397
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] -6.41 -0.08 -0.15 14.03 -0.1 -7.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.077 r_dihedral_angle_4_deg 18.731 r_dihedral_angle_3_deg 18.722 r_dihedral_angle_1_deg 6.556 r_angle_refined_deg 1.482 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.077 r_dihedral_angle_4_deg 18.731 r_dihedral_angle_3_deg 18.722 r_dihedral_angle_1_deg 6.556 r_angle_refined_deg 1.482 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.101 r_bond_refined_d 0.014 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 62912 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 282
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling