5A93

293K Joint X-ray Neutron with Cefotaxime: EXPLORING THE MECHANISM OF BETA-LACTAM RING PROTONATION IN THE CLASS A BETA-LACTAMASE ACYLATION MECHANISM USING NEUTRON AND X-RAY CRYSTALLOGRAPHY


NEUTRON DIFFRACTION - X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XR0PDB ENTRY 2XR0PDB ENTRY 2XR0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.9
26.1
Crystal Properties
Matthews coefficientSolvent content
2.7354.91
2.7354.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.315α = 90
b = 73.315β = 90
c = 98.87γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS IV++2010-04-05MSINGLE WAVELENGTH
22neutron293SNS ANGER CAMERAORNL ANGER CAMERAMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.54
2NUCLEAR REACTORORNL Spallation Neutron Source BEAMLINE MANDI3.0ORNL Spallation Neutron SourceMANDI

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)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
11.619.599.50.0776.16.841094
22.215.2171.40.1710.179.43.911803
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.680.2972.85.8
22.22.280.2523.92.2

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.59819.5031.3441055206699.530.13450.13340.1562
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.215.031157957472.260.2180.21710.2363
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
f_dihedral_angle_d19.221
f_angle_d1.248
f_chiral_restr0.087
f_bond_d0.012
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1961
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms51

Software

Software
Software NamePurpose
CNSphasing
PHENIXrefinement
Mantiddata reduction
Mantiddata scaling
d*TREKdata reduction
d*TREKdata scaling