2GDN

Crystal structure of the Mycobacterium tuberculosis beta-lactamase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BSGPDB ENTRY 1BSG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82890.1 M Tris-HCl, 2.0 M NH4H2PO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2946.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.744α = 90
b = 71.283β = 90
c = 85.169γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray121CCDADSC QUANTUM 3152004-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90APS14-BM-C

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
11.7254.6491.10.11110.76.825908-3
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)
1.721.781001000.3066.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1BSG1.7254.642590825858128891.020.1820.180.213RANDOM20.729
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]
1.8-1.42-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.227
r_dihedral_angle_4_deg20.995
r_dihedral_angle_3_deg12.946
r_dihedral_angle_1_deg7.854
r_scangle_it3.312
r_scbond_it2.166
r_angle_refined_deg1.426
r_mcangle_it1.241
r_mcbond_it0.776
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.227
r_dihedral_angle_4_deg20.995
r_dihedral_angle_3_deg12.946
r_dihedral_angle_1_deg7.854
r_scangle_it3.312
r_scbond_it2.166
r_angle_refined_deg1.426
r_mcangle_it1.241
r_mcbond_it0.776
r_nbtor_refined0.304
r_symmetry_vdw_refined0.247
r_symmetry_hbond_refined0.214
r_nbd_refined0.211
r_xyhbond_nbd_refined0.132
r_chiral_restr0.109
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1988
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing