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Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Dibekacin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IQA PDB 5IQA
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 55.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.99 α = 90 b = 98.34 β = 105.24 c = 93.22 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 2016-08-23 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) Rrim I (All) Rpim I (All) 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 2.6 98.34 100 0.162 0.194 0.132 0.978 4.7 3.7 48468 46.543
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.68 99.8 1.072 1.273 0.856 0.358 1.2 3.5
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 PDB 5IQA 2.6 89.94 46011 2438 99.92 0.19445 0.19183 0.1954 0.24395 0.2494 RANDOM 61.529
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] 0.01 -0.05 -0.23 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.72 r_dihedral_angle_3_deg 14.998 r_dihedral_angle_4_deg 14.431 r_dihedral_angle_1_deg 5.689 r_long_range_B_refined 5.127 r_long_range_B_other 5.124 r_scangle_other 2.931 r_mcangle_it 2.498 r_mcangle_other 2.498 r_angle_refined_deg 1.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.72 r_dihedral_angle_3_deg 14.998 r_dihedral_angle_4_deg 14.431 r_dihedral_angle_1_deg 5.689 r_long_range_B_refined 5.127 r_long_range_B_other 5.124 r_scangle_other 2.931 r_mcangle_it 2.498 r_mcangle_other 2.498 r_angle_refined_deg 1.836 r_scbond_it 1.806 r_scbond_other 1.806 r_mcbond_it 1.561 r_mcbond_other 1.561 r_angle_other_deg 1.041 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 9486 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 259
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling Coot model building REFMAC phasing