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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 2.14 42.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.805 α = 90 b = 81.626 β = 118.28 c = 32.358 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 1.55 40.8 98.8 0.031 0.042 22.1 3.2 20312 20192 21.5
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 1.55 1.63 95.5 0.085 0.085 8.8 2.5 2840
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 2JCP 1.55 40.8 20133 1028 98.75 0.1819 0.1801 0.1776 0.215 0.2134 RANDOM 13.8573
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] -0.67 -0.55 0.46 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.266 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 11.87 r_dihedral_angle_1_deg 7.02 r_scangle_it 4.373 r_scbond_it 2.711 r_mcangle_it 1.727 r_angle_refined_deg 1.523 r_mcbond_it 1.014 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.266 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 11.87 r_dihedral_angle_1_deg 7.02 r_scangle_it 4.373 r_scbond_it 2.711 r_mcangle_it 1.727 r_angle_refined_deg 1.523 r_mcbond_it 1.014 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1171 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 25
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction JDirector data collection XDS data reduction