6Y8L

Mycobacterium thermoresistibile GyrB21 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 100 mM zinc chloride, 100 mM ammonium acetate, 3.5-5% (w/v) PEG6000, 3.5-5% (w/v) PEG8000, 3.5-5% (w/v) PEG1000 and 100 mM Bis-Tris pH 7.0-7.3
Crystal Properties
Matthews coefficientSolvent content
2.2144.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.962α = 90
b = 51.114β = 100.32
c = 83.205γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9700DiamondI03

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
11.481.861000.0480.0520.020.99915.76.571663
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)
11.41.421000.8750.9560.380.8496.2

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 REPLACEMENTTHROUGHOUT4B6C1.481.8667991364999.960.1420.13990.1813RANDOM24.977
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]
1.030.16-0.97-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.144
r_dihedral_angle_4_deg18.797
r_dihedral_angle_3_deg12.427
r_dihedral_angle_1_deg5.969
r_rigid_bond_restr2.579
r_angle_refined_deg1.513
r_angle_other_deg1.432
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.144
r_dihedral_angle_4_deg18.797
r_dihedral_angle_3_deg12.427
r_dihedral_angle_1_deg5.969
r_rigid_bond_restr2.579
r_angle_refined_deg1.513
r_angle_other_deg1.432
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2817
Nucleic Acid Atoms
Solvent Atoms296
Heterogen Atoms147

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing