7O5Q

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Oxacillin


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 at 1:1 ratio.
Crystal Properties
Matthews coefficientSolvent content
2.7154.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.053α = 90
b = 126.902β = 98.289
c = 111.201γ = 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
11.8519.8199.90.997106.9109814
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)
11.851.880.7251.2

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-VALUE4S2P1.8519.807109782546599.8640.1750.17310.211127.894
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]
3.9630.53-2.548-1.505
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.164
r_dihedral_angle_4_deg17.442
r_dihedral_angle_3_deg13.699
r_dihedral_angle_1_deg6.039
r_lrange_it5.858
r_lrange_other5.778
r_scangle_it4.775
r_scangle_other4.775
r_scbond_it3.092
r_scbond_other3.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.164
r_dihedral_angle_4_deg17.442
r_dihedral_angle_3_deg13.699
r_dihedral_angle_1_deg6.039
r_lrange_it5.858
r_lrange_other5.778
r_scangle_it4.775
r_scangle_other4.775
r_scbond_it3.092
r_scbond_other3.092
r_mcangle_it2.92
r_mcangle_other2.919
r_mcbond_it2.11
r_mcbond_other2.109
r_angle_refined_deg1.631
r_angle_other_deg1.31
r_nbd_other0.297
r_nbd_refined0.205
r_symmetry_nbd_refined0.179
r_symmetry_xyhbond_nbd_refined0.165
r_symmetry_nbd_other0.162
r_nbtor_refined0.158
r_xyhbond_nbd_refined0.15
r_chiral_restr_other0.09
r_chiral_restr0.081
r_symmetry_nbtor_other0.075
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 Atoms7932
Nucleic Acid Atoms
Solvent Atoms703
Heterogen Atoms167

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing