7SY9

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A5Fpdb entry 5a5f in two domains as per Morda

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5287Molecular dimensions/Calibre Morpheus screen, condition G6: 10% (w/V) PEG 8000, 20% (V/V) ethylene glycol: 20mM of each sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, potassium sodium tartrate tetrahydrate, sodium oxamate: 100mM Sodium HEPES: MOPS (acid) pH 7.5: PsaeA.17938.a.B2.PS38064 at 46mg/ml: tray 320910 g6: cryo: direct: puck hdj1-6.
Crystal Properties
Matthews coefficientSolvent content
2.9858.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.75α = 90
b = 94.75β = 90
c = 442.92γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97741ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.755099.70.0680.072120.7910.5383198474.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.821000.6010.6290.9373.5611.486

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEpdb entry 5a5f in two domains as per Morda2.7547.381.3631899202199.840.21410.21190.2467081.4
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.5127
f_angle_d0.7179
f_chiral_restr0.0476
f_plane_restr0.0063
f_bond_d0.0044
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6173
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms10

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing
Cootmodel building
PHENIXmodel building