2UWX

Active site restructuring regulates ligand recognition in class A penicillin-binding proteins


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BG1PDB ENTRY 2BG1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1750 MM HEPES PH7 0.8 M AMMONIUM SULFATE 2.8 M SODIUM CHLORIDE, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
3.1861

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.52α = 90
b = 148.65β = 90
c = 98.02γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
12.42099.90.0725.6425660-3
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)
12.42.5990.314.83.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2BG12.3981.6525660281999.70.1680.1620.218RANDOM33.3
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]
-0.610.89-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.627
r_dihedral_angle_3_deg15.702
r_dihedral_angle_4_deg15.492
r_dihedral_angle_1_deg6.685
r_scangle_it4.239
r_scbond_it2.823
r_angle_refined_deg1.753
r_mcangle_it1.608
r_mcbond_it0.984
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.627
r_dihedral_angle_3_deg15.702
r_dihedral_angle_4_deg15.492
r_dihedral_angle_1_deg6.685
r_scangle_it4.239
r_scbond_it2.823
r_angle_refined_deg1.753
r_mcangle_it1.608
r_mcbond_it0.984
r_nbtor_refined0.298
r_nbd_refined0.21
r_xyhbond_nbd_refined0.173
r_symmetry_hbond_refined0.172
r_symmetry_vdw_refined0.159
r_chiral_restr0.116
r_bond_refined_d0.02
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3634
Nucleic Acid Atoms
Solvent Atoms322
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing