7OUM

BDM88855 inhibitor bound to the transmembrane domain of AcrB-R971A


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, 0.13-0.2M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000, 0.006M BDM88855
Crystal Properties
Matthews coefficientSolvent content
3.968.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.214α = 90
b = 161.631β = 90
c = 244.437γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-02-14MSINGLE 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)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
12.4549.511000.2810.2920.0780.9976.513.9212143
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.491002.052.1270.5650.59314

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 REPLACEMENTTHROUGHOUT5JMN2.4549.512015671046899.980.22940.2280.2555RANDOM49.147
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]
0.190.07-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.604
r_dihedral_angle_4_deg14.288
r_dihedral_angle_3_deg13.407
r_dihedral_angle_1_deg4.902
r_angle_refined_deg1.169
r_angle_other_deg1.033
r_chiral_restr0.032
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.604
r_dihedral_angle_4_deg14.288
r_dihedral_angle_3_deg13.407
r_dihedral_angle_1_deg4.902
r_angle_refined_deg1.169
r_angle_other_deg1.033
r_chiral_restr0.032
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25894
Nucleic Acid Atoms
Solvent Atoms671
Heterogen Atoms519

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
REFMACphasing