4EYL

Crystal structure of NDM-1 bound to hydrolyzed meropenem


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52981M trisodium cacodylate, 0.1M sodium cacodylate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2645.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106α = 90
b = 106β = 90
c = 92.58γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2011-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-1CLSI08B1-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.942.1996.140390-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9292.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.942.193999038311203095.80.1860.1840.224RANDOM17.86
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]
0.280.28-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.826
r_dihedral_angle_4_deg21.11
r_dihedral_angle_3_deg14.474
r_dihedral_angle_1_deg7.638
r_scangle_it6.419
r_scbond_it4.453
r_mcangle_it2.845
r_angle_refined_deg1.977
r_mcbond_it1.888
r_chiral_restr0.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.826
r_dihedral_angle_4_deg21.11
r_dihedral_angle_3_deg14.474
r_dihedral_angle_1_deg7.638
r_scangle_it6.419
r_scbond_it4.453
r_mcangle_it2.845
r_angle_refined_deg1.977
r_mcbond_it1.888
r_chiral_restr0.125
r_gen_planes_refined0.019
r_bond_refined_d0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3500
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms58

Software

Software
Software NamePurpose
MxDCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling