7NRJ

Crystal Structure of a Class D carbapenemase complexed with iodide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4S2P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1M HEPES pH 8.0, 10% PEG 8000, 10% 1-BUTANOL mixed with the 10 mg/mL protein stock in 0.1M HEPES pH 7.5 buffer at 1:1 ratio
Crystal Properties
Matthews coefficientSolvent content
2.6954.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.764α = 90
b = 126.86β = 98.354
c = 111.1γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2020-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.979150SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.6719.7899.90.996116.8147826
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.671.70.6461

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 REPLACEMENTFREE R-VALUE4S2P1.6719.741147791745099.8490.1680.1660.196624.36
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]
3.0980.985-2.398-0.948
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.296
r_dihedral_angle_4_deg17.041
r_dihedral_angle_3_deg12.465
r_dihedral_angle_1_deg5.869
r_lrange_it5.73
r_lrange_other5.531
r_scangle_it4.454
r_scangle_other4.454
r_scbond_it2.875
r_scbond_other2.874
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.296
r_dihedral_angle_4_deg17.041
r_dihedral_angle_3_deg12.465
r_dihedral_angle_1_deg5.869
r_lrange_it5.73
r_lrange_other5.531
r_scangle_it4.454
r_scangle_other4.454
r_scbond_it2.875
r_scbond_other2.874
r_mcangle_other2.501
r_mcangle_it2.5
r_mcbond_it1.811
r_mcbond_other1.808
r_angle_refined_deg1.602
r_angle_other_deg1.35
r_nbd_refined0.211
r_xyhbond_nbd_refined0.163
r_symmetry_nbd_other0.162
r_nbtor_refined0.157
r_symmetry_nbd_refined0.155
r_nbd_other0.145
r_symmetry_xyhbond_nbd_refined0.133
r_chiral_restr0.082
r_symmetry_nbtor_other0.073
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7923
Nucleic Acid Atoms
Solvent Atoms921
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing