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Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) in complex with GMPPNP, Magnesium, and Ribostamycin
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 2.87 56.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.22 α = 90 b = 99.67 β = 104.9 c = 93.4 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 ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal 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) R Sym 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 2.1 90.26 99.7 0.095 0.127 0.995 8 4.1 92940 37.3
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 2.1 2.14 95.2 1.187 1 3.2
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 2.2 90.26 77029 4078 99.91 0.16434 0.16234 0.17 0.20214 0.2082 RANDOM 46.315
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] -0.42 -0.58 1.05 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.266 r_dihedral_angle_3_deg 13.859 r_dihedral_angle_4_deg 13.082 r_long_range_B_refined 9.41 r_long_range_B_other 9.387 r_dihedral_angle_1_deg 5.844 r_scangle_other 4.531 r_mcangle_it 3.024 r_mcangle_other 3.024 r_scbond_it 2.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.266 r_dihedral_angle_3_deg 13.859 r_dihedral_angle_4_deg 13.082 r_long_range_B_refined 9.41 r_long_range_B_other 9.387 r_dihedral_angle_1_deg 5.844 r_scangle_other 4.531 r_mcangle_it 3.024 r_mcangle_other 3.024 r_scbond_it 2.849 r_scbond_other 2.848 r_mcbond_it 1.976 r_mcbond_other 1.975 r_angle_refined_deg 1.639 r_angle_other_deg 1.358 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.007 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 9726 Nucleic Acid Atoms Solvent Atoms 1098 Heterogen Atoms 263
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling REFMAC phasing Coot model building