4P8W

The crystal structures of YKL-39 in the presence of chitooligosaccharides (GlcNAc4) were solved to resolutions of 1.9 angstrom


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298PEG 3350, Lithium sulfate, Bis Tris
Crystal Properties
Matthews coefficientSolvent content
2.1542.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.354α = 90
b = 71.354β = 90
c = 140.528γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105CCDADSC QUANTUM 3152012-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8719.89945.17.426230
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)
11.871.987.80.1942.85.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.8719.826230140389.940.188010.185560.23595RANDOM24.564
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]
0.380.38-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.128
r_dihedral_angle_4_deg20.922
r_dihedral_angle_3_deg15.136
r_dihedral_angle_1_deg6.012
r_long_range_B_refined5.576
r_long_range_B_other5.315
r_scangle_other3.331
r_mcangle_it2.215
r_mcangle_other2.215
r_scbond_it2.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.128
r_dihedral_angle_4_deg20.922
r_dihedral_angle_3_deg15.136
r_dihedral_angle_1_deg6.012
r_long_range_B_refined5.576
r_long_range_B_other5.315
r_scangle_other3.331
r_mcangle_it2.215
r_mcangle_other2.215
r_scbond_it2.012
r_scbond_other2.01
r_mcbond_it1.446
r_mcbond_other1.445
r_angle_refined_deg1.372
r_angle_other_deg0.792
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2888
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement