4OX9

Crystal structure of the aminoglycoside resistance methyltransferase NpmA bound to the 30S ribosomal subunit


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J5EPDB ENTRY 1J5E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527714% MPD, 0.2 M KCL , 75 mM NH4Cl, 15 mM MgCl2 , 0.1M MES
2VAPOR DIFFUSION, HANGING DROP727714% MPD, 0.2 M KCL , 75 mM NH4Cl, 15 mM MgCl2 , 0.1M MES
Crystal Properties
Matthews coefficientSolvent content
4.5572.98
4.5572.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 403.52α = 90
b = 403.52β = 90
c = 176.61γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-06-26MSINGLE WAVELENGTH
22100
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97APS24-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.85099.80.120.12813.228.89142385-380
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)RedundancyNumber Unique Reflections (All)
13.83.999.91.4381.5251.43

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUEPDB ENTRY 1J5E3.803549.7151.34141742703499.660.2340.23280.2568Inherited 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
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.371
f_angle_d1.292
f_chiral_restr0.106
f_plane_restr0.015
f_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20984
Nucleic Acid Atoms32394
Solvent Atoms
Heterogen Atoms149

Software

Software
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction