8VEP

Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 acylated by piperacillin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6VBC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.829132-40% PEG 600, 0.1 M CHES
Crystal Properties
Matthews coefficientSolvent content
2.345.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.621α = 90
b = 61.621β = 90
c = 110.534γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
1246.0799.30.1770.0740.999.96.62383916.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0798.50.5520.2460.8292.35.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.00246.0723837115899.30.1720.170.206RANDOM17.513
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]
0.73-0.9920.262
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.379
r_dihedral_angle_3_deg13.271
r_dihedral_angle_2_deg9.466
r_dihedral_angle_1_deg6.651
r_lrange_it4.968
r_lrange_other4.935
r_scangle_it3.65
r_scangle_other3.649
r_mcangle_it2.442
r_mcangle_other2.441
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.379
r_dihedral_angle_3_deg13.271
r_dihedral_angle_2_deg9.466
r_dihedral_angle_1_deg6.651
r_lrange_it4.968
r_lrange_other4.935
r_scangle_it3.65
r_scangle_other3.649
r_mcangle_it2.442
r_mcangle_other2.441
r_scbond_it2.267
r_scbond_other2.266
r_angle_refined_deg1.613
r_mcbond_it1.581
r_mcbond_other1.581
r_angle_other_deg0.5
r_nbd_refined0.209
r_symmetry_nbd_other0.18
r_nbtor_refined0.176
r_symmetry_xyhbond_nbd_refined0.176
r_xyhbond_nbd_refined0.157
r_nbd_other0.096
r_symmetry_nbtor_other0.088
r_chiral_restr0.073
r_symmetry_nbd_refined0.055
r_bond_refined_d0.008
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 Atoms2453
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
REFMACphasing