2YHY

Structure of N-Acetylmannosamine kinase in complex with N- acetylmannosamine and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EO3PDB ENTRY 3EO3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2 M CALCIUM ACETATE, 0.1M SODIUM CACODYLATE PH 6.5, 40% PEG 300.
Crystal Properties
Matthews coefficientSolvent content
2.8256.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.38α = 90
b = 90.38β = 90
c = 101.16γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.82501000.0534.0712.84899254.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.921000.694.4

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 3EO31.8241.263627219091000.153720.152280.18163RANDOM31.605
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]
0.170.17-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.459
r_dihedral_angle_4_deg27.329
r_dihedral_angle_3_deg14.88
r_dihedral_angle_1_deg6.18
r_scangle_it5.613
r_scbond_it3.532
r_mcangle_it2.146
r_angle_refined_deg2.097
r_mcbond_it1.279
r_angle_other_deg1.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.459
r_dihedral_angle_4_deg27.329
r_dihedral_angle_3_deg14.88
r_dihedral_angle_1_deg6.18
r_scangle_it5.613
r_scbond_it3.532
r_mcangle_it2.146
r_angle_refined_deg2.097
r_mcbond_it1.279
r_angle_other_deg1.094
r_mcbond_other0.461
r_chiral_restr0.128
r_bond_refined_d0.025
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2269
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing