4BYH | pdb_00004byh

Crystal structure of sialylated IgG Fc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AVEPDB ENTRY 3AVE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
144M NACL, 0.1 M CITRATE PH 4.0
Crystal Properties
Matthews coefficientSolvent content
4.0169.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153α = 90
b = 153β = 90
c = 111.85γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.36699.50.0717.78.734456-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3699.30.772.88.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3AVE2.366.3432683174599.010.224260.222230.230.261650.26RANDOM66.114
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]
-1.67-1.67-1.675.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.431
r_dihedral_angle_4_deg21.312
r_dihedral_angle_3_deg17.033
r_dihedral_angle_1_deg6.432
r_mcangle_it3.154
r_scbond_it2.332
r_mcbond_it1.823
r_mcbond_other1.822
r_angle_refined_deg1.501
r_angle_other_deg1.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.431
r_dihedral_angle_4_deg21.312
r_dihedral_angle_3_deg17.033
r_dihedral_angle_1_deg6.432
r_mcangle_it3.154
r_scbond_it2.332
r_mcbond_it1.823
r_mcbond_other1.822
r_angle_refined_deg1.501
r_angle_other_deg1.159
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3330
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms253

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
SCALAdata scaling
PHASERphasing