4P8X

The crystal structures of YKL-39 in the presence of chitooligosaccharides (GlcNAc6) were solved to resolutions of 2.48 angstrom


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298PEG 3350, Lithium sulfate, Bis Tris
Crystal Properties
Matthews coefficientSolvent content
1.9642.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.207α = 90
b = 71.207β = 90
c = 141.023γ = 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)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
12.4824.899.60.15116.812681
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)
12.482.5494.60.353.15.3

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 DIFFRACTIONTHROUGHOUT2.4824.81263068798.520.189530.18710.23471RANDOM50.017
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]
2.422.42-4.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.128
r_dihedral_angle_4_deg21.175
r_dihedral_angle_3_deg19.987
r_long_range_B_refined7.119
r_long_range_B_other7.103
r_dihedral_angle_1_deg6.551
r_scangle_other5.102
r_mcangle_it4.633
r_mcangle_other4.631
r_scbond_it3.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.128
r_dihedral_angle_4_deg21.175
r_dihedral_angle_3_deg19.987
r_long_range_B_refined7.119
r_long_range_B_other7.103
r_dihedral_angle_1_deg6.551
r_scangle_other5.102
r_mcangle_it4.633
r_mcangle_other4.631
r_scbond_it3.24
r_scbond_other3.214
r_mcbond_it3.104
r_mcbond_other3.104
r_angle_refined_deg1.513
r_angle_other_deg0.802
r_chiral_restr0.08
r_bond_refined_d0.011
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 Atoms2894
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement