3QBW

Crystal structure of pseudomonas aeruginosa 1,6-anhydro-n-actetylmuramic acid kinase (ANMK) bound to adenosine diphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CQY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629625% PEG 4000, 0.2 M (NH4)2SO4, 0.1 M tri-Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.5651.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.218α = 90
b = 90.218β = 90
c = 174.82γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002010-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9795CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.2346.711000.0820.08716.78.65630839204336
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.232.3599.80.3970.434.66.85683

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3CQY2.2346.713920437465169199.780.188840.188840.187830.21034RANDOM35.154
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]
-10.95-10.9521.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.586
r_dihedral_angle_4_deg17.296
r_dihedral_angle_3_deg14.164
r_dihedral_angle_1_deg5.374
r_scangle_it2.529
r_scbond_it1.531
r_angle_refined_deg1.173
r_mcangle_it0.969
r_mcbond_it0.514
r_chiral_restr0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.586
r_dihedral_angle_4_deg17.296
r_dihedral_angle_3_deg14.164
r_dihedral_angle_1_deg5.374
r_scangle_it2.529
r_scbond_it1.531
r_angle_refined_deg1.173
r_mcangle_it0.969
r_mcbond_it0.514
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5228
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms64

Software

Software
Software NamePurpose
MxDCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling