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Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) in complex with GMPPCP and Magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IQA APH(2'')-Ia GMPPNP-Mg complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 296 80-120mM MgCl2, 8% Glycerol, 10% PEG3350, 100mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.84 56.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.29 α = 90 b = 99.9 β = 105.09 c = 93.62 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX-300 2013-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
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 2.15 58.92 95 0.091 12.3 3.9 82837
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 2.15 2.19 65.6 0.532 2.6 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT APH(2'')-Ia GMPPNP-Mg complex 2.15 58.92 78653 4159 94.86 0.15805 0.1559 0.19828 0.2107 RANDOM 47.77
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.214 r_dihedral_angle_4_deg 14.056 r_dihedral_angle_3_deg 12.548 r_long_range_B_refined 8.568 r_long_range_B_other 8.565 r_dihedral_angle_1_deg 5.747 r_scangle_other 5.12 r_angle_other_deg 3.576 r_scbond_it 3.342 r_scbond_other 3.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.214 r_dihedral_angle_4_deg 14.056 r_dihedral_angle_3_deg 12.548 r_long_range_B_refined 8.568 r_long_range_B_other 8.565 r_dihedral_angle_1_deg 5.747 r_scangle_other 5.12 r_angle_other_deg 3.576 r_scbond_it 3.342 r_scbond_other 3.341 r_mcangle_it 3.197 r_mcangle_other 3.197 r_mcbond_it 2.273 r_mcbond_other 2.273 r_angle_refined_deg 1.582 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_other 0.016 r_gen_planes_refined 0.008 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9741 Nucleic Acid Atoms Solvent Atoms 1059 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling Coot model building REFMAC phasing