2XH9

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) PEG4000,0.1M NAAC,0.1M NACL,10%(W/V) GLYCEROL,0.1M TRIS/HCL PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.514α = 90
b = 100.895β = 93.94
c = 81.355γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM16ESRFBM16

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
11.881.198.10.13.789909
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)
11.81.8691.30.253.1

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 2XEP1.881.1185397449798.090.198620.197060.22821RANDOM22.061
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]
-0.75-0.50.7-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.895
r_dihedral_angle_4_deg15.887
r_dihedral_angle_3_deg12.894
r_dihedral_angle_1_deg5.476
r_scangle_it3.5
r_scbond_it2.226
r_angle_refined_deg1.768
r_mcangle_it1.341
r_mcbond_it0.853
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.895
r_dihedral_angle_4_deg15.887
r_dihedral_angle_3_deg12.894
r_dihedral_angle_1_deg5.476
r_scangle_it3.5
r_scbond_it2.226
r_angle_refined_deg1.768
r_mcangle_it1.341
r_mcbond_it0.853
r_nbtor_refined0.302
r_nbd_refined0.198
r_symmetry_vdw_refined0.145
r_xyhbond_nbd_refined0.125
r_symmetry_hbond_refined0.111
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.006
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 Atoms6538
Nucleic Acid Atoms
Solvent Atoms639
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing