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Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Lividomycin moieties
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 56.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.25 α = 90 b = 100.24 β = 105.17 c = 94.01 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) 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 2.4 90.73 100 0.11 0.127 0.084 0.988 10 4.2 63302 50.686
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 2.4 2.46 100 1.345 1.538 1.011 0.287 1.8 4.2
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 PDB 5IQA 2.4 90.73 60081 3190 99.93 0.17368 0.1714 0.1772 0.21598 0.217 RANDOM 59.493
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] -0.15 -0.05 0.16 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.121 r_dihedral_angle_4_deg 15.753 r_dihedral_angle_3_deg 14.669 r_long_range_B_other 6.892 r_long_range_B_refined 6.88 r_dihedral_angle_1_deg 6.085 r_scangle_other 4.481 r_mcangle_it 3.056 r_mcangle_other 3.056 r_scbond_it 2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.121 r_dihedral_angle_4_deg 15.753 r_dihedral_angle_3_deg 14.669 r_long_range_B_other 6.892 r_long_range_B_refined 6.88 r_dihedral_angle_1_deg 6.085 r_scangle_other 4.481 r_mcangle_it 3.056 r_mcangle_other 3.056 r_scbond_it 2.89 r_scbond_other 2.89 r_mcbond_it 2.071 r_mcbond_other 2.071 r_angle_refined_deg 2.038 r_angle_other_deg 1.073 r_chiral_restr 0.123 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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 9588 Nucleic Acid Atoms Solvent Atoms 541 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling Coot model building