6LBL

Crystal structure of IMP-1 metallo-beta-lactamase in complex with NO9 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EV6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29330% PEG 3350, 0.2M sodium acetate, 0.1M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.0339.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.92α = 90
b = 56.61β = 90
c = 100.62γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAichiSR BEAMLINE BL2S11.12AichiSRBL2S1

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
11.6856.6199.70.06718.98.824088
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)
11.681.7799.90.2818.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5ev61.6849.38624038118799.590.160.15770.20825.78
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]
-0.2571.241-0.984
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.428
r_dihedral_angle_4_deg20.678
r_dihedral_angle_3_deg14.929
r_dihedral_angle_1_deg7.739
r_lrange_other7.268
r_lrange_it7.265
r_dihedral_angle_other_3_deg6.705
r_scangle_it6.054
r_scangle_other6.051
r_scbond_it4.259
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.428
r_dihedral_angle_4_deg20.678
r_dihedral_angle_3_deg14.929
r_dihedral_angle_1_deg7.739
r_lrange_other7.268
r_lrange_it7.265
r_dihedral_angle_other_3_deg6.705
r_scangle_it6.054
r_scangle_other6.051
r_scbond_it4.259
r_scbond_other4.259
r_mcangle_it3.569
r_mcangle_other3.568
r_mcbond_it2.639
r_mcbond_other2.632
r_angle_refined_deg1.528
r_angle_other_deg1.338
r_symmetry_xyhbond_nbd_refined0.255
r_nbd_other0.227
r_nbd_refined0.22
r_symmetry_nbd_other0.199
r_symmetry_nbd_refined0.188
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.168
r_symmetry_xyhbond_nbd_other0.111
r_chiral_restr0.079
r_symmetry_nbtor_other0.079
r_metal_ion_refined0.044
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1728
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing