6NTJ

Neutron/X-ray crystal structure of AAC-VIa bound to gentamicin C1A


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6BBZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293polyethylene glycol (PEG) 8000, 0.2 M MgCl2, 0.1 M Tris, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.6253.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.319α = 90
b = 86.228β = 120.4
c = 51.003γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS IV++2018-01-01MSINGLE WAVELENGTH
21neutron293AREA DETECTORORNL ANGER CAMERA2018-01-01LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418
2NUCLEAR REACTORORNL Spallation Neutron Source BEAMLINE MANDI2.0-4.0ORNL Spallation Neutron SourceMANDI

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (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
11.95098.40.0560.0680.03918.82.82600234.34
22.3516.876.90.1170.1460.0850.98982.61067734.34
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.970.6580.8220.4840.6712.6
11.972.050.5180.6460.3790.7262.8
12.052.140.360.4470.260.852.8
12.142.250.260.3220.1860.9062.8
12.252.390.1760.2170.1260.9512.8
12.392.580.1270.1570.0910.9772.8
12.582.840.0830.1030.0590.9882.8
12.843.250.0520.0640.0370.9952.9
13.254.090.0350.0430.0240.9972.9
14.09500.0370.0450.0250.9963
22.352.480.290.2042.5

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.943.1141.3425996130498.270.15880.15660.199754.987
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.3516.81067553576.080.26710.26480.3092
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2022
Nucleic Acid Atoms
Solvent Atoms452
Heterogen Atoms77

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing