6Q4N

Fusidic acid bound AcrB_V340A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JMN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.62910.05M ADA, pH 6.6, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000
Crystal Properties
Matthews coefficientSolvent content
3.6866.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.208α = 90
b = 162.986β = 90
c = 245.638γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2016-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.98SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.849.131000.2127.57.7143625
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.851.773

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5JMN2.849.09136414710599.970.234480.232880.2651RANDOM60.575
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]
-4.652.941.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.711
r_dihedral_angle_4_deg16.598
r_dihedral_angle_3_deg15.522
r_dihedral_angle_1_deg4.993
r_long_range_B_refined2.948
r_long_range_B_other2.948
r_mcangle_it1.278
r_mcangle_other1.278
r_angle_refined_deg1.188
r_angle_other_deg1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.711
r_dihedral_angle_4_deg16.598
r_dihedral_angle_3_deg15.522
r_dihedral_angle_1_deg4.993
r_long_range_B_refined2.948
r_long_range_B_other2.948
r_mcangle_it1.278
r_mcangle_other1.278
r_angle_refined_deg1.188
r_angle_other_deg1.05
r_scangle_other0.931
r_mcbond_it0.693
r_mcbond_other0.693
r_scbond_it0.492
r_scbond_other0.492
r_chiral_restr0.036
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25923
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms826

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing