1H8Y

Crystal structure of the class D beta-lactamase OXA-13 in complex with meropenem


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherTHE STARTING MODEL USED WAS THE ONE OF OXA-13

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.515-17% (W/V) PEG 4000, 0.1M SODIUM CACODYLATE PH 5.0-5.5, 0.2M LITHIUM SULFATE, PROTEIN 12-15 MG/ML
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.34α = 90
b = 112.3β = 90
c = 124.98γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42000-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
123097.70.09215.56.5430032.5
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)
122.187.80.3991.52.2

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHE STARTING MODEL USED WAS THE ONE OF OXA-1323040758217297.70.2040.257RANDOM31.3
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor30.5
p_staggered_tor17.1
p_scangle_it5.356
p_planar_tor4.5
p_mcangle_it3.981
p_scbond_it3.738
p_mcbond_it3.054
p_multtor_nbd0.266
p_chiral_restr0.183
p_singtor_nbd0.183
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor30.5
p_staggered_tor17.1
p_scangle_it5.356
p_planar_tor4.5
p_mcangle_it3.981
p_scbond_it3.738
p_mcbond_it3.054
p_multtor_nbd0.266
p_chiral_restr0.183
p_singtor_nbd0.183
p_planar_d0.035
p_plane_restr0.028
p_angle_d0.025
p_bond_d0.024
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_xyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3870
Nucleic Acid Atoms
Solvent Atoms324
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing