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Crystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form D)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G96 PDB ENTRY 4G96
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 22.5 % (w/v) PEG 3,350, 0.2 M ammonium sulfate and 0.1 M MES pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.8 56.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.289 α = 95.26 b = 65.098 β = 88.88 c = 106.78 γ = 89.62
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 ADSC QUANTUM 315r 2009-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9745 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.48 50 94.8 47011 46992
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 2.48 2.57 74.9 0.294 2.04 1.9
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 (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 4G96 2.48 36.31 47011 46992 2376 94.6 0.2099 0.2082 0.2179 0.2427 0.2553 THIN 31.648
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] 10.6373 -5.6882 1.9514 -5.0703 -6.1692 -5.567
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.2 t_omega_torsion 3.6 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.2 t_omega_torsion 3.6 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8527 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 20
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction GDA data collection DENZO data reduction BUSTER refinement