6P53

Crystal structure of the transpeptidase domain of PBP2 from Neisseria gonorrhoeae in apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4U3TPDB entry 4U3T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.329140% PEG600, 0.1 M CHES
Crystal Properties
Matthews coefficientSolvent content
2.1843.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.334α = 90
b = 77.254β = 91.85
c = 88.007γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-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
11.9236.0990.80.0520.022133.96.34214126
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)
11.921.9597.30.4130.1910.933.35.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4U3T1.9236.0940127198790.560.1840.1810.229RANDOM33.881
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]
2.440.82-0.91-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.924
r_dihedral_angle_4_deg15.713
r_dihedral_angle_3_deg13.558
r_dihedral_angle_1_deg6.292
r_long_range_B_refined5.238
r_long_range_B_other5.218
r_scangle_other3.753
r_mcangle_it2.992
r_mcangle_other2.992
r_scbond_it2.365
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.924
r_dihedral_angle_4_deg15.713
r_dihedral_angle_3_deg13.558
r_dihedral_angle_1_deg6.292
r_long_range_B_refined5.238
r_long_range_B_other5.218
r_scangle_other3.753
r_mcangle_it2.992
r_mcangle_other2.992
r_scbond_it2.365
r_scbond_other2.364
r_mcbond_it2.024
r_mcbond_other2.023
r_angle_refined_deg1.437
r_angle_other_deg0.803
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4860
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms5

Software

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