6KXI

Crystal Structure Of NDM-1 Metallo-beta-lactamase In Complex With Inhibitor NO9


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EYB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2M Ammonium Sulfate, 0.1M Bis-Tris [pH 6.1], 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0439.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.55α = 90
b = 73.66β = 90
c = 77.75γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.00Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.3842.6241000.10816.91283907
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.381.451000.20512.1

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4eyb1.3842.62483827415999.9930.1370.13620.157311.041
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]
0.093-0.1050.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.251
r_dihedral_angle_4_deg23.865
r_dihedral_angle_3_deg14.002
r_dihedral_angle_1_deg13.17
r_dihedral_angle_other_3_deg10.542
r_lrange_it5.179
r_lrange_other5.062
r_scangle_other3.214
r_scangle_it3.212
r_mcangle_it2.347
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.251
r_dihedral_angle_4_deg23.865
r_dihedral_angle_3_deg14.002
r_dihedral_angle_1_deg13.17
r_dihedral_angle_other_3_deg10.542
r_lrange_it5.179
r_lrange_other5.062
r_scangle_other3.214
r_scangle_it3.212
r_mcangle_it2.347
r_mcangle_other2.347
r_scbond_other2.114
r_scbond_it2.113
r_angle_refined_deg1.569
r_angle_other_deg1.489
r_mcbond_it1.433
r_mcbond_other1.427
r_nbd_other0.218
r_nbd_refined0.214
r_symmetry_nbd_refined0.208
r_symmetry_nbd_other0.195
r_nbtor_refined0.169
r_symmetry_xyhbond_nbd_refined0.161
r_xyhbond_nbd_refined0.15
r_symmetry_nbtor_other0.086
r_chiral_restr0.077
r_symmetry_xyhbond_nbd_other0.076
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_gen_planes_other0.001
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3466
Nucleic Acid Atoms
Solvent Atoms628
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing