6BBZ

Room temperature neutron/X-ray structure of sisomicin bound AAC-VIa


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6BC6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52850.1 M Tris, pH 8.5, 0.3 M magnesium chloride, 15-17% PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.5952.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.822α = 90
b = 86.169β = 94.55
c = 76.9γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKU RAXIS IV++2017-07-01MSINGLE WAVELENGTH
21neutron298DIFFRACTOMETERORNL ANGER CAMERA2017-07-01LLAUE
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
11.95099.250.0470.0670.0470.99717.21.662587432.2
22.215.5792.20.1480.1730.0870.97910.23.41586032.2
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)
11.91.970.4010.5110.3130.8392.1
11.972.050.3210.4060.2460.8862.4
12.052.140.2430.3070.1850.9262.4
12.142.250.1650.2080.1250.9632.4
12.252.390.1270.1610.0970.9782.4
12.392.580.0890.1120.0670.9892.4
12.582.840.0650.0810.0490.9922.4
12.843.250.0450.0560.0330.9962.4
13.254.090.0310.0380.0230.9982.5
14.09500.0310.0380.0230.9972.4

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 REPLACEMENT1.938.3291.3425867128699.230.15190.15030.1814
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.215.4331551276392.470.19870.19760.2199
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_d19.476
f_dihedral_angle_d19.476
f_angle_d0.81
f_angle_d0.81
f_chiral_restr0.074
f_chiral_restr0.074
f_bond_d0.013
f_bond_d0.013
f_plane_restr0.004
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2023
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms32

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing