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Crystal structure of the human CD23 Lectin domain, apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DV8 A MODIFIED VERSION OF PDB ENTRY 1DV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 1.2 M sodium monobasic phosphate, 0.8 M potassium dibasic phosphate, 0.1 M Caps buffer pH 10.5, and 0.2 M
lithium sulfate; final pH 6.2 , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.354 α = 90 b = 50.667 β = 127.09 c = 75.061 γ = 90
Symmetry Space Group C 1 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 113 CCD MARRESEARCH 2003-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.97895 APS 5ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 30 99.5 0.051 18.7 7 53947 53947 24.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.66 99.8 0.281 6.3 7.4 14045
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 A MODIFIED VERSION OF PDB ENTRY 1DV8 1.5 59.87 51219 51219 2727 99.85 0.12562 0.12562 0.12353 0.124 0.16481 0.1659 THIN SHELLS 20.547
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] -0.71 -0.46 0.24 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.505 r_sphericity_free 22.32 r_dihedral_angle_3_deg 13.568 r_dihedral_angle_4_deg 12.903 r_scangle_it 9.247 r_sphericity_bonded 8.995 r_scbond_it 7.468 r_mcangle_it 7.01 r_dihedral_angle_1_deg 6.771 r_mcbond_it 6.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.505 r_sphericity_free 22.32 r_dihedral_angle_3_deg 13.568 r_dihedral_angle_4_deg 12.903 r_scangle_it 9.247 r_sphericity_bonded 8.995 r_scbond_it 7.468 r_mcangle_it 7.01 r_dihedral_angle_1_deg 6.771 r_mcbond_it 6.33 r_rigid_bond_restr 4.669 r_mcbond_other 3.966 r_angle_refined_deg 1.449 r_angle_other_deg 0.768 r_symmetry_vdw_other 0.269 r_nbd_other 0.222 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.219 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.183 r_symmetry_vdw_refined 0.182 r_chiral_restr 0.11 r_nbtor_other 0.094 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2193 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling CNS phasing