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Aminoglycoside Phosphotransferase (2'')-Ia S376N mutant in complex with GMPPNP and Magnesium
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 56.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.43 α = 90 b = 99.91 β = 105.17 c = 93.2 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 2014-02-25 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 2.3 58.89 100 0.133 0.155 0.104 0.987 9.7 4.3 71190 44.012
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 2.3 2.35 100 0.965 1.11 0.741 0.434 1.9 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 2.3 58.89 67572 3596 99.96 0.17209 0.17008 0.1764 0.2097 0.2125 RANDOM 51.437
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] -0.02 -0.03 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.21 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_4_deg 14.35 r_long_range_B_refined 6.807 r_long_range_B_other 6.804 r_dihedral_angle_1_deg 5.957 r_scangle_other 4.58 r_mcangle_it 3.317 r_mcangle_other 3.316 r_scbond_it 2.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.21 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_4_deg 14.35 r_long_range_B_refined 6.807 r_long_range_B_other 6.804 r_dihedral_angle_1_deg 5.957 r_scangle_other 4.58 r_mcangle_it 3.317 r_mcangle_other 3.316 r_scbond_it 2.978 r_scbond_other 2.978 r_mcbond_it 2.239 r_mcbond_other 2.239 r_angle_refined_deg 2.014 r_angle_other_deg 1.065 r_chiral_restr 0.124 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 9608 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling Coot model building