8BTU

Structure of D179N BlaC from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.1 M ammonium acetate; 0.1 M BIS-TRIS buffer; 17% w/v PEG 10K
Crystal Properties
Matthews coefficientSolvent content
1.9537.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.37α = 90
b = 54.05β = 93.2
c = 53.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9795DiamondI04-1

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
11.838.3498.40.0910.9885.21.820045
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)
11.81.8497.70.4270.5911.2

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 REPLACEMENTTHROUGHOUT2GDN1.838.3419002104398.040.183560.180510.2379RANDOM18.087
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]
0.380.560.43-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.848
r_dihedral_angle_1_deg7.015
r_dihedral_angle_2_deg6.402
r_long_range_B_refined4.394
r_long_range_B_other4.177
r_scangle_other2.595
r_mcangle_it2.073
r_mcangle_other2.073
r_scbond_it1.731
r_scbond_other1.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.848
r_dihedral_angle_1_deg7.015
r_dihedral_angle_2_deg6.402
r_long_range_B_refined4.394
r_long_range_B_other4.177
r_scangle_other2.595
r_mcangle_it2.073
r_mcangle_other2.073
r_scbond_it1.731
r_scbond_other1.73
r_mcbond_it1.323
r_mcbond_other1.318
r_angle_refined_deg1.313
r_angle_other_deg0.438
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1992
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing