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Aminoglycoside Phosphotransferase (2'')-Ia (CTD of APH(6')-Ie/APH(2'')-Ia) in complex with GDP and Magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 296 80-120mM MgCl2, 8% glycerol, 10% PEG 3350, 100mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.78 55.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.454 α = 90 b = 99.075 β = 105.18 c = 92.35 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 RIGAKU SATURN 944+ 2016-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.35 89.13 100 0.139 0.997 10.9 7.2 65601 35.1
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 2.35 2.41 100 1.211 1.7 6.9
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 FOURIER SYNTHESIS THROUGHOUT 5BYL 2.35 89.13 62255 3318 99.94 0.18244 0.18001 0.1848 0.22783 0.2307 RANDOM 49.218
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 34.872 r_dihedral_angle_4_deg 16.933 r_dihedral_angle_3_deg 15.169 r_long_range_B_refined 7.691 r_long_range_B_other 7.658 r_dihedral_angle_1_deg 5.523 r_scangle_other 3.801 r_angle_other_deg 3.606 r_mcangle_it 2.53 r_mcangle_other 2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.872 r_dihedral_angle_4_deg 16.933 r_dihedral_angle_3_deg 15.169 r_long_range_B_refined 7.691 r_long_range_B_other 7.658 r_dihedral_angle_1_deg 5.523 r_scangle_other 3.801 r_angle_other_deg 3.606 r_mcangle_it 2.53 r_mcangle_other 2.53 r_scbond_it 2.404 r_scbond_other 2.404 r_mcbond_it 1.638 r_mcbond_other 1.637 r_angle_refined_deg 1.537 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 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 9817 Nucleic Acid Atoms Solvent Atoms 921 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling Coot model building REFMAC phasing