6CGD

Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Amikacin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529680-120mM MgCl2, 8% glycerol, 10% PEG 3350, 100mM HEPES pH 7.5
Crystal Properties
Matthew coefficientSolvent content
2.8756.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.08α = 90
b = 100.22β = 105.12
c = 93.99γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002013-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9795CLSI08ID-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.290.741000.1150.1340.0890.99110.54.38190310.563
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)RedundancyNumber Unique Reflections (All)
12.22.241001.0221.1690.5571.84.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB 5IQA2.290.7477748412899.950.173780.171910.20893RANDOM50.781
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]
0.07-0.050.02-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.466
r_dihedral_angle_3_deg13.628
r_dihedral_angle_4_deg13.238
r_long_range_B_other7.849
r_long_range_B_refined7.849
r_dihedral_angle_1_deg5.939
r_scangle_other5.084
r_mcangle_it3.457
r_mcangle_other3.457
r_scbond_it3.279
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.466
r_dihedral_angle_3_deg13.628
r_dihedral_angle_4_deg13.238
r_long_range_B_other7.849
r_long_range_B_refined7.849
r_dihedral_angle_1_deg5.939
r_scangle_other5.084
r_mcangle_it3.457
r_mcangle_other3.457
r_scbond_it3.279
r_scbond_other3.279
r_mcbond_it2.355
r_mcbond_other2.355
r_angle_refined_deg1.658
r_angle_other_deg1.354
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.008
r_gen_planes_other0.007
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9788
Nucleic Acid Atoms
Solvent Atoms634
Heterogen Atoms219

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
Cootmodel building