6P52

Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae with a bound phosphate at the active site


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
1.9837.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.973α = 90
b = 76.868β = 92.32
c = 86.47γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2017-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
11.8338.3599.60.0710.0290.67842.56.84872530
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)
11.831.8699.20.9320.3940.76426.5

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 4U3T1.8338.3546252243698.40.1970.1950.233RANDOM37.5
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]
0.430.26-0.04-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.565
r_dihedral_angle_4_deg15.053
r_dihedral_angle_3_deg13.136
r_dihedral_angle_1_deg6.064
r_long_range_B_refined4.932
r_long_range_B_other4.878
r_scangle_other3.627
r_mcangle_it2.68
r_mcangle_other2.68
r_scbond_it2.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.565
r_dihedral_angle_4_deg15.053
r_dihedral_angle_3_deg13.136
r_dihedral_angle_1_deg6.064
r_long_range_B_refined4.932
r_long_range_B_other4.878
r_scangle_other3.627
r_mcangle_it2.68
r_mcangle_other2.68
r_scbond_it2.263
r_scbond_other2.255
r_mcbond_it1.874
r_mcbond_other1.872
r_angle_refined_deg1.269
r_angle_other_deg0.761
r_chiral_restr0.074
r_bond_refined_d0.008
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 Atoms4747
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms10

Software

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