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Crystal structure of the aminoglycoside resistance methyltransferase NpmA bound to the 30S ribosomal subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J5E PDB ENTRY 1J5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 14% MPD, 0.2 M KCL , 75 mM NH4Cl, 15 mM MgCl2 , 0.1M MES 2 VAPOR DIFFUSION, HANGING DROP 7 277 14% MPD, 0.2 M KCL , 75 mM NH4Cl, 15 mM MgCl2 , 0.1M MES
Crystal Properties Matthews coefficient Solvent content 4.55 72.98 4.55 72.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 403.52 α = 90 b = 403.52 β = 90 c = 176.61 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-06-26 M SINGLE WAVELENGTH 2 2 100
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.8 50 99.8 0.12 0.128 13.22 8.89 142385 -3 80
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.8 3.9 99.9 1.438 1.525 1.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB ENTRY 1J5E 3.8035 49.715 1.34 141742 7034 99.66 0.234 0.2328 0.2379 0.2568 0.2617 Inherited from 1j5e
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.371 f_angle_d 1.292 f_chiral_restr 0.106 f_plane_restr 0.015 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20984 Nucleic Acid Atoms 32394 Solvent Atoms Heterogen Atoms 149
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction