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Crystal structure of CD5 domain III reveals the fold of a group B scavenger cysteine-rich receptor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 15-25% PEG 8000, 100 MM NAAC PH 4.4, 200 MM LI2SO4
Crystal Properties Matthews coefficient Solvent content 3.7 67.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.931 α = 90 b = 62.931 β = 90 c = 72.564 γ = 120
Symmetry Space Group P 32 2 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 MARRESEARCH 2006-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.21 50 96.9 0.05 15.3 5.4 12098 2
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 2.21 2.26 95.6 0.24 2.2 4.1
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 SAD THROUGHOUT 2.21 19.18 7899 387 95.6 0.196 0.193 0.1893 0.248 0.2373 RANDOM 44.77
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] 0.38 0.19 0.38 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.047 r_dihedral_angle_4_deg 25.84 r_dihedral_angle_3_deg 19.026 r_dihedral_angle_1_deg 12.584 r_scangle_it 9.823 r_scbond_it 7.241 r_mcangle_it 4.863 r_mcbond_it 3.492 r_angle_refined_deg 2.156 r_nbtor_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.047 r_dihedral_angle_4_deg 25.84 r_dihedral_angle_3_deg 19.026 r_dihedral_angle_1_deg 12.584 r_scangle_it 9.823 r_scbond_it 7.241 r_mcangle_it 4.863 r_mcbond_it 3.492 r_angle_refined_deg 2.156 r_nbtor_refined 0.33 r_nbd_refined 0.259 r_xyhbond_nbd_refined 0.215 r_chiral_restr 0.183 r_symmetry_vdw_refined 0.156 r_symmetry_hbond_refined 0.141 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 789 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms
Software Software Software Name Purpose ARP/wARP model building SCALEPACK data scaling BNP phasing SHARP phasing SOLOMON phasing ARP/wARP phasing REFMAC refinement