8VBZ

Crystal structure of the transpeptidase domain of a S310A mutant of PBP2 from Neisseria gonorrhoeae strain H041


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29132-40% PEG 600, 0.1 M CHES
Crystal Properties
Matthews coefficientSolvent content
2.345.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.487α = 90
b = 61.079β = 90
c = 109.419γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2023-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.945.996.60.1070.1160.0450.99120.15.92737220.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9399.40.4910.5330.2040.9082.756.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.945.8825188127596.550.1770.1750.211RANDOM25.9
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]
-2.991.261.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.331
r_dihedral_angle_4_deg19.958
r_dihedral_angle_3_deg13.493
r_dihedral_angle_1_deg6.487
r_long_range_B_refined6.192
r_scbond_it3.504
r_mcangle_it2.835
r_mcbond_it2.167
r_angle_refined_deg1.7
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.331
r_dihedral_angle_4_deg19.958
r_dihedral_angle_3_deg13.493
r_dihedral_angle_1_deg6.487
r_long_range_B_refined6.192
r_scbond_it3.504
r_mcangle_it2.835
r_mcbond_it2.167
r_angle_refined_deg1.7
r_chiral_restr0.109
r_gen_planes_refined0.01
r_bond_refined_d0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2423
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms

Software

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