6OL8

Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q6X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52920.15M KBr, 30% PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
1.8734.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.469α = 90
b = 76.449β = 90
c = 130.906γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918400BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
12.166.0297.60.1490.1690.9974.322766-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2396.60.80.920.623.9

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 REPLACEMENTFREE R-VALUE3q6x2.121.6521606116097.580.174990.172140.22726RANDOM33.59
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]
-1.570.441.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.176
r_dihedral_angle_4_deg17.608
r_dihedral_angle_3_deg14.026
r_dihedral_angle_1_deg7.393
r_long_range_B_refined6.573
r_long_range_B_other6.571
r_scangle_other4.867
r_scbond_it3.555
r_scbond_other3.554
r_mcangle_other3.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.176
r_dihedral_angle_4_deg17.608
r_dihedral_angle_3_deg14.026
r_dihedral_angle_1_deg7.393
r_long_range_B_refined6.573
r_long_range_B_other6.571
r_scangle_other4.867
r_scbond_it3.555
r_scbond_other3.554
r_mcangle_other3.341
r_mcangle_it3.34
r_mcbond_it2.403
r_mcbond_other2.401
r_angle_refined_deg1.614
r_angle_other_deg1.398
r_chiral_restr0.067
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3566
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing