7PGO

Crystal Structure of a Class D Carbapenemase_R250A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52910.1M HEPES pH 7.5, 11.6% PEG8000, 8% 1-BuOH, mixed with the 10 mg/mL protein stock at 1:1 ratio.
Crystal Properties
Matthews coefficientSolvent content
2.3647.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.546α = 90
b = 108.2β = 90
c = 124.61γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.918395DiamondI03

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
11.8558.751000.9966.623.298044
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)
11.851.880.7371.1

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 REPLACEMENTFREE R-VALUE4S2P1.8558.7597955502299.9140.2070.20520.23420.915
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]
2.548-0.76-1.788
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.622
r_dihedral_angle_4_deg15.909
r_dihedral_angle_3_deg13.713
r_dihedral_angle_1_deg6.027
r_lrange_it5.395
r_lrange_other5.313
r_scangle_it3.453
r_scangle_other3.452
r_mcangle_it2.943
r_mcangle_other2.943
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.622
r_dihedral_angle_4_deg15.909
r_dihedral_angle_3_deg13.713
r_dihedral_angle_1_deg6.027
r_lrange_it5.395
r_lrange_other5.313
r_scangle_it3.453
r_scangle_other3.452
r_mcangle_it2.943
r_mcangle_other2.943
r_scbond_it2.149
r_scbond_other2.149
r_mcbond_it1.824
r_mcbond_other1.824
r_angle_refined_deg1.435
r_angle_other_deg1.366
r_symmetry_nbd_refined0.267
r_nbd_other0.22
r_nbd_refined0.218
r_symmetry_nbd_other0.171
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.166
r_symmetry_xyhbond_nbd_refined0.151
r_symmetry_nbtor_other0.076
r_ncsr_local_group_50.074
r_chiral_restr0.073
r_ncsr_local_group_30.071
r_ncsr_local_group_20.07
r_ncsr_local_group_40.07
r_ncsr_local_group_60.057
r_ncsr_local_group_10.051
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7956
Nucleic Acid Atoms
Solvent Atoms901
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing