☰ Navigation Tabs
The crystal structures of YKL-39 in the presence of chitooligosaccharides (GlcNAc2) were solved to resolutions of 1.5 angstrom
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 PEG 3350, Lithium Sulfate, Bis Tris
Crystal Properties Matthews coefficient Solvent content 2.14 42.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.682 α = 90 b = 70.682 β = 90 c = 140.255 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD ADSC QUANTUM 315 2012-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.53 19.61 99.3 0.075 26.3 11.5 50934
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.56 99.3 0.753 2.8 8.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.64 19.61 41175 2180 98.13 0.17442 0.1728 0.1851 0.2044 0.218 RANDOM 16.899
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] 0.23 0.23 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.821 r_dihedral_angle_4_deg 16.709 r_dihedral_angle_3_deg 14.189 r_long_range_B_refined 6.767 r_dihedral_angle_1_deg 6.157 r_long_range_B_other 5.944 r_scangle_other 1.76 r_mcangle_other 1.428 r_mcangle_it 1.427 r_angle_refined_deg 1.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.821 r_dihedral_angle_4_deg 16.709 r_dihedral_angle_3_deg 14.189 r_long_range_B_refined 6.767 r_dihedral_angle_1_deg 6.157 r_long_range_B_other 5.944 r_scangle_other 1.76 r_mcangle_other 1.428 r_mcangle_it 1.427 r_angle_refined_deg 1.418 r_scbond_it 1.128 r_scbond_other 1.118 r_mcbond_it 0.902 r_mcbond_other 0.898 r_angle_other_deg 0.797 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2895 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement