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The hyaluronan binding domain of murine CD44 in a Type B complex with an HA 8-mer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JCQ PDB ENTRY 2JCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 CO-CRYSTALS OF THE CD44/HA8 COMPLEX WERE PREPARED AFTER ADDITION OF HA8 (2MM FINAL CONCENTRATION) TO THE 0.5 MM PROTEIN SOLUTION FOLLOWED BY MIXING 1:1 WITH WELL SOLUTIONS CONTAINING 25% (W/V) PEG 3350 AND 100MM NACL IN 100MM HEPES BUFFERED AT PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.8 α = 90 b = 82.1 β = 118 c = 32.4 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD BRUKER MIRRORS 2005-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR
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 2 28.6 92.3 0.11 10.4 2.5 9641
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 2 2.05 67.5 0.24 3.6 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2JCQ 2 28.61 8114 407 88.5 0.179 0.175 0.1792 0.254 0.2582 RANDOM 9.88
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] -0.97 -0.88 0.78 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.989 r_dihedral_angle_4_deg 16.704 r_dihedral_angle_3_deg 14.059 r_dihedral_angle_1_deg 6.667 r_sphericity_free 3.04 r_scangle_it 2.161 r_scbond_it 1.382 r_angle_refined_deg 1.28 r_sphericity_bonded 0.923 r_angle_other_deg 0.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.989 r_dihedral_angle_4_deg 16.704 r_dihedral_angle_3_deg 14.059 r_dihedral_angle_1_deg 6.667 r_sphericity_free 3.04 r_scangle_it 2.161 r_scbond_it 1.382 r_angle_refined_deg 1.28 r_sphericity_bonded 0.923 r_angle_other_deg 0.855 r_mcangle_it 0.755 r_rigid_bond_restr 0.711 r_mcbond_it 0.559 r_symmetry_vdw_other 0.255 r_nbd_refined 0.196 r_nbd_other 0.195 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.184 r_nbtor_refined 0.172 r_mcbond_other 0.164 r_xyhbond_nbd_refined 0.161 r_nbtor_other 0.081 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1172 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement PROTEUM data reduction SAINT data reduction SADABS data scaling XSCALE data scaling MOLREP phasing