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Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Amikacin
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 56.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.08 α = 90 b = 100.22 β = 105.12 c = 93.99 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 2.2 90.74 100 0.115 0.134 0.089 0.991 10.5 4.3 81903 10.563
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 100 1.022 1.169 0.557 1.8 4.3
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 2.2 90.74 77748 4128 99.95 0.17378 0.17191 0.1786 0.20893 0.2131 RANDOM 50.781
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] 0.07 -0.05 0.02 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.466 r_dihedral_angle_3_deg 13.628 r_dihedral_angle_4_deg 13.238 r_long_range_B_refined 7.849 r_long_range_B_other 7.849 r_dihedral_angle_1_deg 5.939 r_scangle_other 5.084 r_mcangle_it 3.457 r_mcangle_other 3.457 r_scbond_it 3.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.466 r_dihedral_angle_3_deg 13.628 r_dihedral_angle_4_deg 13.238 r_long_range_B_refined 7.849 r_long_range_B_other 7.849 r_dihedral_angle_1_deg 5.939 r_scangle_other 5.084 r_mcangle_it 3.457 r_mcangle_other 3.457 r_scbond_it 3.279 r_scbond_other 3.279 r_mcbond_it 2.355 r_mcbond_other 2.355 r_angle_refined_deg 1.658 r_angle_other_deg 1.354 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.008 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 9788 Nucleic Acid Atoms Solvent Atoms 634 Heterogen Atoms 219
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling Coot model building