4P8U

The crystal structures of YKL-39 in the absence of chitooligosaccharides was solved to resolutions of 2.4 angstrom


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298PEG 3350, Lithium sulfate, Bis Tris
Crystal Properties
Matthews coefficientSolvent content
2.0539.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.764α = 90
b = 70.764β = 90
c = 141.179γ = 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
12.426.399.935.67.613746
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)
12.42.4499.90.474.57.6

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 REPLACEMENTFREE R-VALUE2.426.271374670598.720.21730.2160.24274RANDOM66.21
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]
0.580.58-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.529
r_dihedral_angle_4_deg20.379
r_dihedral_angle_3_deg20.032
r_long_range_B_refined9.617
r_long_range_B_other9.564
r_scangle_other7.069
r_mcangle_it6.176
r_mcangle_other6.174
r_dihedral_angle_1_deg5.306
r_scbond_it4.695
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.529
r_dihedral_angle_4_deg20.379
r_dihedral_angle_3_deg20.032
r_long_range_B_refined9.617
r_long_range_B_other9.564
r_scangle_other7.069
r_mcangle_it6.176
r_mcangle_other6.174
r_dihedral_angle_1_deg5.306
r_scbond_it4.695
r_scbond_other4.691
r_mcbond_it4.164
r_mcbond_other4.164
r_angle_refined_deg1.39
r_angle_other_deg0.793
r_chiral_restr0.07
r_bond_refined_d0.013
r_bond_other_d0.005
r_gen_planes_refined0.005
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 Atoms2896
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement