4EYB

Crystal structure of NDM-1 bound to hydrolyzed oxacillin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.52980.2M MgCl2, 25% PEG3350, 0.1M bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8332.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.2α = 90
b = 79.37β = 90
c = 134.15γ = 90
Symmetry
Space GroupP 21 21 21

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
11.1625.4299.6143064-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.161.2398.7

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 REPLACEMENTTHROUGHOUT1.1625.42136465135810715799.50.1360.1350.164RANDOM14.29
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]
0.62-0.3-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.263
r_dihedral_angle_4_deg18.739
r_dihedral_angle_3_deg12.807
r_scangle_it8.674
r_dihedral_angle_1_deg6.328
r_scbond_it6.005
r_mcangle_it4.327
r_mcbond_it2.949
r_rigid_bond_restr2.877
r_angle_refined_deg2.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.263
r_dihedral_angle_4_deg18.739
r_dihedral_angle_3_deg12.807
r_scangle_it8.674
r_dihedral_angle_1_deg6.328
r_scbond_it6.005
r_mcangle_it4.327
r_mcbond_it2.949
r_rigid_bond_restr2.877
r_angle_refined_deg2.143
r_chiral_restr0.126
r_bond_refined_d0.019
r_gen_planes_refined0.014
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3594
Nucleic Acid Atoms
Solvent Atoms405
Heterogen Atoms63

Software

Software
Software NamePurpose
MxDCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling