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CD23 Lectin domain, Calcium 2+-bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H2R PDB ENTRY 2H2R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 17% (w/v) PEG 4000, 100 mM Mes buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 20.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.31 α = 90 b = 51.261 β = 90 c = 58.768 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2004-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 1.02336 APS 32-ID
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 1.3 30 99.4 0.09 41.6 7.5 30523 30523 14.74
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 1.3 1.32 100 0.338 3.5 7.5 1515
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 PDB ENTRY 2H2R 1.3 38.63 28870 28870 1561 99.37 0.16953 0.16953 0.16785 0.1751 0.20045 0.2043 THIN SHELLS 15.865
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] 0.52 -0.56 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.961 r_sphericity_free 18.203 r_dihedral_angle_4_deg 17.542 r_dihedral_angle_3_deg 11.692 r_sphericity_bonded 7.9 r_scangle_it 7.473 r_dihedral_angle_1_deg 6.723 r_scbond_it 6.069 r_mcangle_it 5.828 r_mcbond_it 4.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.961 r_sphericity_free 18.203 r_dihedral_angle_4_deg 17.542 r_dihedral_angle_3_deg 11.692 r_sphericity_bonded 7.9 r_scangle_it 7.473 r_dihedral_angle_1_deg 6.723 r_scbond_it 6.069 r_mcangle_it 5.828 r_mcbond_it 4.997 r_rigid_bond_restr 3.762 r_mcbond_other 3.363 r_angle_other_deg 2.527 r_angle_refined_deg 1.658 r_symmetry_vdw_other 0.4 r_xyhbond_nbd_other 0.251 r_symmetry_hbond_refined 0.237 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.227 r_nbd_other 0.222 r_xyhbond_nbd_refined 0.203 r_nbtor_refined 0.194 r_chiral_restr 0.099 r_nbtor_other 0.087 r_metal_ion_refined 0.031 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling CNS phasing