3AVE

Crystal Structure of the Fucosylated Fc Fragment from Human Immunoglobulin G1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DTQPDB ENTRY 2DTQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS7277deionized water, 20% 2,3-butanediol, pH 7.0, MICRODIALYSIS, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7855.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.419α = 90
b = 78.471β = 90
c = 143.758γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102005-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32B21.0000SPring-8BL32B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12501000.0860.09312.573871238712-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.111000.6770.733.37.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2DTQ240.723-3386443864419351000.187570.184830.23904RANDOM41.11
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]
-0.02-0.040.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.25
r_dihedral_angle_4_deg15.193
r_dihedral_angle_3_deg14.782
r_dihedral_angle_1_deg6.44
r_scangle_it5.69
r_scbond_it4.078
r_mcangle_it2.868
r_mcbond_it1.841
r_angle_refined_deg1.672
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.25
r_dihedral_angle_4_deg15.193
r_dihedral_angle_3_deg14.782
r_dihedral_angle_1_deg6.44
r_scangle_it5.69
r_scbond_it4.078
r_mcangle_it2.868
r_mcbond_it1.841
r_angle_refined_deg1.672
r_nbtor_refined0.313
r_nbd_refined0.2
r_symmetry_hbond_refined0.157
r_symmetry_vdw_refined0.146
r_xyhbond_nbd_refined0.134
r_chiral_restr0.103
r_symmetry_metal_ion_refined0.029
r_bond_refined_d0.017
r_metal_ion_refined0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3348
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms199

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling