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Crystal structure of the murine CD44 hyaluronan binding domain complex with a small molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JCP pdb entry 2JCP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 30% PEG MME 5000, 100 mM MES, 200 mM (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.987 α = 90 b = 81.744 β = 118.21 c = 32.236 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 PIXEL DECTRIS PILATUS 6M 2012-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
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 1.12 81.74 97.7 0.036 0.049 16.7 3.2 53169 52863 12.2
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) 1 1.12 1.18 94.7 0.159 0.159 4.5 3 7454
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2JCP 1.12 40.87 52824 2706 97.5 0.1699 0.1691 0.1838 0.1909 RANDOM 11.8071
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] -0.14 -0.34 -0.02 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.343 r_dihedral_angle_4_deg 19.484 r_dihedral_angle_3_deg 11.029 r_dihedral_angle_1_deg 7.314 r_scangle_it 3.812 r_scbond_it 2.423 r_mcangle_it 1.628 r_angle_refined_deg 1.541 r_mcbond_it 0.935 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.343 r_dihedral_angle_4_deg 19.484 r_dihedral_angle_3_deg 11.029 r_dihedral_angle_1_deg 7.314 r_scangle_it 3.812 r_scbond_it 2.423 r_mcangle_it 1.628 r_angle_refined_deg 1.541 r_mcbond_it 0.935 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1171 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 14
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction JDirector data collection XDS data reduction