2XFT

Structural and mechanistic studies on a cephalosporin esterase from the clavulanic acid biosynthesis pathway


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XEPPDB ENTRY 2XEP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1813%(W/V) PEG 4000, 0.1M NAAC, 0.1M NACL, 10%(W/V) GLYCEROL, 0.1 M TRIS/HCL PH 8
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.068α = 90
b = 100.056β = 93.64
c = 81.271γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42009-01-29MSINGLE 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
11.881.11000.064.290179
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)
11.81.861000.223.4

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 DIFFRACTIONMIRTHROUGHOUTPDB ENTRY 2XEP1.881.1185628452399.980.196130.194020.23623RANDOM19.567
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]
-0.03-0.490.75-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.634
r_dihedral_angle_4_deg15.87
r_dihedral_angle_3_deg13.131
r_dihedral_angle_1_deg5.546
r_scangle_it3.45
r_scbond_it2.231
r_angle_refined_deg1.395
r_mcangle_it1.324
r_mcbond_it0.856
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.634
r_dihedral_angle_4_deg15.87
r_dihedral_angle_3_deg13.131
r_dihedral_angle_1_deg5.546
r_scangle_it3.45
r_scbond_it2.231
r_angle_refined_deg1.395
r_mcangle_it1.324
r_mcbond_it0.856
r_nbtor_refined0.301
r_nbd_refined0.2
r_symmetry_vdw_refined0.162
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.118
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.005
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 Atoms6509
Nucleic Acid Atoms
Solvent Atoms585
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing