9QI5 | pdb_00009qi5

Crystal structure of I105R mutant of 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 DROP4.0829122%v/v PEGSM, 0.2M Na Acetate, 0.024M Zn Chloride
Crystal Properties
Matthews coefficientSolvent content
1.8934.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.161α = 90
b = 40.975β = 90
c = 267.495γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 9M2023-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.8731ESRFID30B

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
11.844.6298.60.9958.21.840588
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)
11.81.840.5891.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.844.6238570201898.310.17540.17350.18540.211180.2216RANDOM26.433
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]
0.760.2-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.638
r_dihedral_angle_2_deg7.586
r_dihedral_angle_1_deg6.677
r_long_range_B_refined4.846
r_long_range_B_other4.779
r_scangle_other2.836
r_scbond_it1.82
r_scbond_other1.82
r_mcangle_it1.675
r_mcangle_other1.674
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.638
r_dihedral_angle_2_deg7.586
r_dihedral_angle_1_deg6.677
r_long_range_B_refined4.846
r_long_range_B_other4.779
r_scangle_other2.836
r_scbond_it1.82
r_scbond_other1.82
r_mcangle_it1.675
r_mcangle_other1.674
r_angle_refined_deg1.524
r_mcbond_it1.117
r_mcbond_other1.117
r_angle_other_deg0.54
r_chiral_restr0.077
r_bond_refined_d0.007
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 Atoms3987
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
Aimlessdata scaling