7P9Y

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


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 Na-HEPES/MOPS pH 7.5; 12.5% each MPD, PEG 1K, PEG 3350 Condition B8 of Morpheus screen (Molecular Dimensions)
Crystal Properties
Matthews coefficientSolvent content
2.5150.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.476α = 90
b = 115.476β = 90
c = 119.657γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-08-05MSINGLE 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
11.9457.741000.999116.768568
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)
11.941.990.282

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-VALUE4DB31.9446.13668526351799.9750.2110.2090.249755.854
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]
0.2880.1440.288-0.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.908
r_dihedral_angle_4_deg16.51
r_dihedral_angle_3_deg16.205
r_lrange_it15.956
r_scangle_it14.513
r_scbond_it12.064
r_mcangle_it11.197
r_mcbond_it9.215
r_dihedral_angle_1_deg6.278
r_angle_refined_deg1.654
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.908
r_dihedral_angle_4_deg16.51
r_dihedral_angle_3_deg16.205
r_lrange_it15.956
r_scangle_it14.513
r_scbond_it12.064
r_mcangle_it11.197
r_mcbond_it9.215
r_dihedral_angle_1_deg6.278
r_angle_refined_deg1.654
r_nbtor_refined0.313
r_symmetry_nbd_refined0.244
r_nbd_refined0.227
r_xyhbond_nbd_refined0.126
r_symmetry_xyhbond_nbd_refined0.114
r_chiral_restr0.11
r_ncsr_local_group_10.085
r_bond_refined_d0.009
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4630
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms143

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
DMphasing
MOLREPphasing
BUSTERrefinement