9IBA | pdb_00009iba

Crystal structure of Arr-2 in complex with Rifampicin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52955 mg/ml, 1 mM inhibitor (7-chloro-2-{4-[(2-hydroxyethyl)(methyl)amino]phenyl}-3,4-dihydroquinazolin-4-one), 1 mM rifampicin, 100 mM MOPS pH 7.5, 20% ethanol, and 2.7 M (NH4)2 SO4.
Crystal Properties
Matthews coefficientSolvent content
2.2244.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.26α = 90
b = 42.97β = 90
c = 85.49γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2024-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.96546ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.45099.60.99812.415.0130653
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4499.80.7842.125.12

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.438.42330602153199.6390.1450.14310.1430.18460.184222.01
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]
-0.266-0.1930.459
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.931
r_dihedral_angle_3_deg12.257
r_dihedral_angle_4_deg10.798
r_dihedral_angle_1_deg7.059
r_lrange_it5.717
r_lrange_other5.59
r_scangle_other5.113
r_scangle_it5.109
r_scbond_it4.349
r_scbond_other4.339
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.931
r_dihedral_angle_3_deg12.257
r_dihedral_angle_4_deg10.798
r_dihedral_angle_1_deg7.059
r_lrange_it5.717
r_lrange_other5.59
r_scangle_other5.113
r_scangle_it5.109
r_scbond_it4.349
r_scbond_other4.339
r_mcangle_other3.513
r_mcangle_it3.502
r_mcbond_it2.78
r_rigid_bond_restr2.706
r_mcbond_other2.658
r_angle_refined_deg1.662
r_angle_other_deg1.367
r_symmetry_nbd_refined0.225
r_nbd_other0.215
r_nbd_refined0.21
r_symmetry_nbd_other0.191
r_nbtor_refined0.177
r_symmetry_xyhbond_nbd_refined0.124
r_xyhbond_nbd_refined0.115
r_symmetry_nbtor_other0.085
r_chiral_restr0.081
r_gen_planes_refined0.013
r_bond_refined_d0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1155
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing