7P9L

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine-6-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DB3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH29190 mM halogens; 0.1 M Tris/bicine pH 8.5; 30% each PEG 550 MME and PEG 20K, condition B9 from Morpheus screen (Molecular Dimensions)
Crystal Properties
Matthews coefficientSolvent content
3.4264.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.508α = 90
b = 114.508β = 90
c = 119.266γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.7599.1799.10.9988.43.890389
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.780.194

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-VALUE4DB31.7576.25290350456899.020.1940.19290.222636.515
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]
-0.012-0.006-0.0120.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.837
r_dihedral_angle_4_deg15.786
r_dihedral_angle_3_deg15.214
r_lrange_it11.616
r_scangle_it10.111
r_scbond_it8.059
r_mcangle_it7.299
r_mcbond_it6.253
r_dihedral_angle_1_deg5.724
r_angle_refined_deg1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.837
r_dihedral_angle_4_deg15.786
r_dihedral_angle_3_deg15.214
r_lrange_it11.616
r_scangle_it10.111
r_scbond_it8.059
r_mcangle_it7.299
r_mcbond_it6.253
r_dihedral_angle_1_deg5.724
r_angle_refined_deg1.75
r_metal_ion_refined0.345
r_nbtor_refined0.318
r_symmetry_nbd_refined0.23
r_nbd_refined0.214
r_xyhbond_nbd_refined0.139
r_chiral_restr0.112
r_symmetry_xyhbond_nbd_refined0.111
r_ncsr_local_group_10.093
r_bond_refined_d0.012
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4646
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms200

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
DMphasing
MOLREPphasing