2H2R

Crystal structure of the human CD23 Lectin domain, apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DV8A MODIFIED VERSION OF PDB ENTRY 1DV8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.22931.2 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 coefficientSolvent content
2.1843.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.354α = 90
b = 50.667β = 127.09
c = 75.061γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMARRESEARCH2003-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 5ID-B0.97895APS5ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.53099.50.05118.77539475394724.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.6699.80.2816.37.414045

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTA MODIFIED VERSION OF PDB ENTRY 1DV81.559.875121951219272799.850.125620.125620.123530.16481THIN SHELLS20.547
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]
-0.71-0.460.24-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.505
r_sphericity_free22.32
r_dihedral_angle_3_deg13.568
r_dihedral_angle_4_deg12.903
r_scangle_it9.247
r_sphericity_bonded8.995
r_scbond_it7.468
r_mcangle_it7.01
r_dihedral_angle_1_deg6.771
r_mcbond_it6.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.505
r_sphericity_free22.32
r_dihedral_angle_3_deg13.568
r_dihedral_angle_4_deg12.903
r_scangle_it9.247
r_sphericity_bonded8.995
r_scbond_it7.468
r_mcangle_it7.01
r_dihedral_angle_1_deg6.771
r_mcbond_it6.33
r_rigid_bond_restr4.669
r_mcbond_other3.966
r_angle_refined_deg1.449
r_angle_other_deg0.768
r_symmetry_vdw_other0.269
r_nbd_other0.222
r_nbd_refined0.221
r_symmetry_hbond_refined0.219
r_nbtor_refined0.193
r_xyhbond_nbd_refined0.183
r_symmetry_vdw_refined0.182
r_chiral_restr0.11
r_nbtor_other0.094
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2193
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
CNSphasing