6Y8O

Mycobacterium smegmatis GyrB 22kDa ATPase sub-domain in complex with novobiocin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B6C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6293Crystals grown with 17 mg/ml protein in the presence of 1 mM novobiocin against 15% (w/v) PEG8000, 100 mM sodium acetate pH 5.6, 200 mM calcium acetate were harvested in the precipitant supplemented with 25% (v/v) ethylene glycol for cryoprotection.
Crystal Properties
Matthews coefficientSolvent content
2.3146.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.962α = 90
b = 56.112β = 90.66
c = 50.678γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

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
11.678.481000.110.1190.0460.99910.46.658273
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)
11.61.631001.0711.1590.440.6476.8

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 REPLACEMENTTHROUGHOUT4B6C1.678.4855300297399.950.13670.1340.188RANDOM21.903
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]
-1.78-0.270.391.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.331
r_dihedral_angle_4_deg16.154
r_dihedral_angle_3_deg12.131
r_dihedral_angle_1_deg6.015
r_rigid_bond_restr2.672
r_angle_refined_deg1.514
r_angle_other_deg1.428
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.331
r_dihedral_angle_4_deg16.154
r_dihedral_angle_3_deg12.131
r_dihedral_angle_1_deg6.015
r_rigid_bond_restr2.672
r_angle_refined_deg1.514
r_angle_other_deg1.428
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2931
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms141

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing