8ECF

Cryo structure of Mycobacterium tuberculosis beta lactamase microcrystals mixed with sulbactam for 3 hours


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6B5X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.13002.1 M Ammonium Phosphate
Crystal Properties
Matthews coefficientSolvent content
3.5765.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.442α = 90
b = 96.666β = 108.082
c = 111.028γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.26APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.648.331000.180.3722.725400
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.640.18

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6b5x2.73648.3325399132260.0320.2140.21110.268257.967
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]
-1.683-0.8962.150.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.443
r_dihedral_angle_6_deg15.141
r_dihedral_angle_2_deg13.509
r_lrange_it11.725
r_lrange_other11.718
r_dihedral_angle_1_deg9.369
r_scangle_it5.646
r_scangle_other5.646
r_mcangle_it4.92
r_mcangle_other4.919
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.443
r_dihedral_angle_6_deg15.141
r_dihedral_angle_2_deg13.509
r_lrange_it11.725
r_lrange_other11.718
r_dihedral_angle_1_deg9.369
r_scangle_it5.646
r_scangle_other5.646
r_mcangle_it4.92
r_mcangle_other4.919
r_scbond_it3.331
r_scbond_other3.331
r_mcbond_it3.008
r_mcbond_other3.006
r_angle_refined_deg1.191
r_angle_other_deg0.417
r_nbd_other0.252
r_symmetry_nbd_refined0.245
r_xyhbond_nbd_refined0.236
r_nbd_refined0.216
r_symmetry_xyhbond_nbd_refined0.216
r_symmetry_nbd_other0.198
r_nbtor_refined0.172
r_ncsr_local_group_40.112
r_ncsr_local_group_10.11
r_ncsr_local_group_60.107
r_ncsr_local_group_30.106
r_ncsr_local_group_20.101
r_ncsr_local_group_50.099
r_symmetry_nbtor_other0.081
r_symmetry_xyhbond_nbd_other0.068
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7952
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing