6EX7

Crystal structure of NDM-1 metallo-beta-lactamase in complex with Cd ions and a hydrolyzed beta-lactam ligand - new refinement


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2890.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25 % PEG 3350, 5 mM CdCl2,10 mM faropenum, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0539.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.062α = 90
b = 39.22β = 99.99
c = 75.233γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97934APS19-ID

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
11.9574.291.7215.62.927008
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952662.22.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFREE R-VALUE1.9574.227008135391.720.196080.19450.20.225880.2copied from entry 4hky32.627
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]
1.680.59-1.25-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.516
r_sphericity_bonded29.68
r_dihedral_angle_4_deg21.945
r_dihedral_angle_3_deg14.174
r_long_range_B_other6.959
r_long_range_B_refined6.955
r_dihedral_angle_1_deg6.295
r_scangle_other4.826
r_scbond_it3.568
r_scbond_other3.56
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3498
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing