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Crystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form A)
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 4.7 298 16 % (w/v) PEG 6,000, 2 % (v/v) 1,6-hexanediol, 0.05 M ammonium sulfate and 0.1 M sodium acetate pH 4.7 , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.691 α = 68.45 b = 56.863 β = 87.83 c = 62.487 γ = 73.56
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 2010-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 1.9 57.96 96.1 50712 48544
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 1.9 15.57 48564 48510 2465 95.56 0.1913 0.1899 0.1903 0.2168 0.2176 RANDOM 40.9941
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] 3.5138 1.7043 -1.256 3.1647 -1.9465 -6.6785
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.55 t_omega_torsion 3.87 t_angle_deg 1.03 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 16.55 t_omega_torsion 3.87 t_angle_deg 1.03 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 4328 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 10
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