2XGN

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
1VAPOR DIFFUSION, SITTING DROP829313%(W/V) PEG4000,0.1M NAAC,0.1M NACL,10%/W/V) GLYCEROL,0.1M TRIS/HCL PH8.0
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.283α = 90
b = 99.765β = 93.97
c = 81.27γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
11.7811000.084.2106976
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)
11.71.761000.413.8

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 2XEP1.781.11101604533499.960.19230.190640.22405RANDOM17.685
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]
0.13-0.170.88-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.402
r_dihedral_angle_4_deg16.27
r_dihedral_angle_3_deg12.675
r_dihedral_angle_1_deg5.344
r_scangle_it3.195
r_scbond_it2.038
r_angle_refined_deg1.339
r_mcangle_it1.226
r_mcbond_it0.764
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.402
r_dihedral_angle_4_deg16.27
r_dihedral_angle_3_deg12.675
r_dihedral_angle_1_deg5.344
r_scangle_it3.195
r_scbond_it2.038
r_angle_refined_deg1.339
r_mcangle_it1.226
r_mcbond_it0.764
r_nbtor_refined0.305
r_nbd_refined0.199
r_symmetry_vdw_refined0.136
r_xyhbond_nbd_refined0.113
r_symmetry_hbond_refined0.1
r_chiral_restr0.088
r_bond_refined_d0.011
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 Atoms6523
Nucleic Acid Atoms
Solvent Atoms755
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing