6H28

Structure of S70A BlaC from Mycobacterium tuberculosis obtained from crystals produced in the absence of DTT


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GDN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1520% w/v PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.1141.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.59α = 101.31
b = 41.7β = 90.02
c = 76.76γ = 90.05
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.975ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.1940.8983.80.0680.9917.43.6458598
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.191.2145.30.4610.4522.12.1

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 REPLACEMENTTHROUGHOUT2GDN1.1940.89121830660883.80.189490.187620.22377RANDOM13.077
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]
-0.75-0.391.620.06-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.596
r_dihedral_angle_4_deg20.647
r_sphericity_free12.6
r_dihedral_angle_3_deg11.777
r_sphericity_bonded9.566
r_dihedral_angle_1_deg6.486
r_rigid_bond_restr4.18
r_scangle_other3.201
r_scbond_it2.931
r_scbond_other2.931
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.596
r_dihedral_angle_4_deg20.647
r_sphericity_free12.6
r_dihedral_angle_3_deg11.777
r_sphericity_bonded9.566
r_dihedral_angle_1_deg6.486
r_rigid_bond_restr4.18
r_scangle_other3.201
r_scbond_it2.931
r_scbond_other2.931
r_long_range_B_other2.892
r_long_range_B_refined2.889
r_mcangle_other2.182
r_mcangle_it2.178
r_angle_refined_deg2.096
r_mcbond_it1.816
r_mcbond_other1.8
r_angle_other_deg1.243
r_chiral_restr0.128
r_bond_refined_d0.018
r_gen_planes_refined0.013
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4076
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing