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Structure of CXCL12:heparin disaccharide complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Soaking 8.5 298 Grown in 2M Ammonium Sulfate, 0.1M TrisHCl pH 8.50. Soaked in 20 mM PEG-8000, 1M TrisHCl pH 8.5, 16 mM disaccharide. , Soaking, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.492 α = 90 b = 56.965 β = 90 c = 71.747 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.07 25.582 99.9 0.057 0.057 31.9 6.3 9627
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.07 2.18 100 0.367 0.367 2 6.5 1385
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 2.07 23.34 9589 459 100 0.241 0.24 0.2352 0.265 0.2606 RANDOM 42.461
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] 0.09 -0.02 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.449 r_dihedral_angle_4_deg 21.32 r_dihedral_angle_3_deg 20.706 r_dihedral_angle_1_deg 8.317 r_angle_refined_deg 2.519 r_scangle_it 2.373 r_mcangle_it 2.255 r_scbond_it 1.654 r_mcbond_it 1.37 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.449 r_dihedral_angle_4_deg 21.32 r_dihedral_angle_3_deg 20.706 r_dihedral_angle_1_deg 8.317 r_angle_refined_deg 2.519 r_scangle_it 2.373 r_mcangle_it 2.255 r_scbond_it 1.654 r_mcbond_it 1.37 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.257 r_symmetry_hbond_refined 0.251 r_xyhbond_nbd_refined 0.222 r_chiral_restr 0.211 r_bond_refined_d 0.025 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1087 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction CCP4 data scaling