1X8I

Crystal Structure of the Zinc Carbapenemase CphA in Complex with the Antibiotic Biapenem


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5280PEG, AS, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.836α = 90
b = 101.513β = 90
c = 117.364γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2003-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.926.593.10.120.123.75.920636
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9699.90.290.292.15.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTCphA (N220G) mutant1.926.519554105199.940.1530.153110.151470.18308RANDOM16.545
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]
0.35-0.28-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.378
r_sphericity_bonded4.489
r_scangle_it4.224
r_sphericity_free3.806
r_scbond_it2.574
r_angle_refined_deg1.748
r_mcangle_it1.461
r_angle_other_deg0.95
r_mcbond_it0.815
r_symmetry_vdw_other0.376
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.378
r_sphericity_bonded4.489
r_scangle_it4.224
r_sphericity_free3.806
r_scbond_it2.574
r_angle_refined_deg1.748
r_mcangle_it1.461
r_angle_other_deg0.95
r_mcbond_it0.815
r_symmetry_vdw_other0.376
r_nbd_refined0.375
r_nbd_other0.246
r_symmetry_vdw_refined0.215
r_xyhbond_nbd_refined0.181
r_symmetry_hbond_refined0.164
r_chiral_restr0.098
r_nbtor_other0.083
r_bond_refined_d0.017
r_gen_planes_other0.016
r_gen_planes_refined0.012
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1754
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms62

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
REFMACrefinement
CCP4data scaling
CCP4phasing