7AJX

The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with meropenem


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7AJ9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2980.1M HEPES pH 7 + 10% PEG 8000 + 10% Ethylene Glycol
Crystal Properties
Matthews coefficientSolvent content
2.9858.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.877α = 90
b = 101.224β = 90
c = 115.285γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979160ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.5546.38699.90.0680.9979.26.722790
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.6699.91.0380.51616.8

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-VALUE7AJ92.5546.3422737110499.8380.2120.2090.26764.039
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]
-5.6890.0875.602
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.661
r_dihedral_angle_4_deg20.052
r_dihedral_angle_3_deg16.968
r_lrange_it9.491
r_lrange_other9.49
r_scangle_it7.476
r_scangle_other7.475
r_dihedral_angle_1_deg7.293
r_mcangle_it6.335
r_mcangle_other6.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.661
r_dihedral_angle_4_deg20.052
r_dihedral_angle_3_deg16.968
r_lrange_it9.491
r_lrange_other9.49
r_scangle_it7.476
r_scangle_other7.475
r_dihedral_angle_1_deg7.293
r_mcangle_it6.335
r_mcangle_other6.335
r_scbond_it4.704
r_scbond_other4.703
r_mcbond_it4.14
r_mcbond_other4.139
r_angle_refined_deg1.452
r_angle_other_deg1.188
r_symmetry_xyhbond_nbd_refined0.227
r_nbd_other0.226
r_nbd_refined0.216
r_symmetry_nbd_other0.193
r_symmetry_nbd_refined0.191
r_xyhbond_nbd_refined0.177
r_nbtor_refined0.166
r_symmetry_nbtor_other0.082
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_symmetry_xyhbond_nbd_other0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3992
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing