8CPB

1,6-anhydro-n-actetylmuramic acid kinase (AnmK) in complex with AMPPNP, and AnhMurNAc at 1.7 Angstroms resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QBWsame protein

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29120% PEG 3350, Na/K tartrate 0.2M
Crystal Properties
Matthews coefficientSolvent content
2.5852.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.67α = 90
b = 90.67β = 90
c = 171.686γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

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
11.746.251000.240.9917.420.787575
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)
11.71.731000.3980.811.920.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.746.24987521423599.9790.1710.16890.204628.328
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]
5.1965.196-10.392
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.12
r_dihedral_angle_3_deg13.747
r_dihedral_angle_1_deg6.385
r_dihedral_angle_2_deg5.396
r_lrange_it3.591
r_lrange_other3.553
r_scangle_it2.296
r_scangle_other2.296
r_mcangle_it1.964
r_mcangle_other1.964
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.12
r_dihedral_angle_3_deg13.747
r_dihedral_angle_1_deg6.385
r_dihedral_angle_2_deg5.396
r_lrange_it3.591
r_lrange_other3.553
r_scangle_it2.296
r_scangle_other2.296
r_mcangle_it1.964
r_mcangle_other1.964
r_scbond_it1.515
r_scbond_other1.515
r_mcbond_it1.285
r_mcbond_other1.284
r_angle_refined_deg1.071
r_angle_other_deg0.707
r_nbd_other0.249
r_nbd_refined0.213
r_symmetry_nbd_refined0.203
r_symmetry_nbd_other0.187
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.142
r_chiral_restr_other0.141
r_symmetry_xyhbond_nbd_refined0.127
r_symmetry_nbtor_other0.075
r_chiral_restr0.055
r_bond_other_d0.017
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5494
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms132

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement