3C2S

Structural Characterization of a Human Fc Fragment Engineered for Lack of Effector Functions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DTQPDB entry 2DTQ, chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION82985% PEG 3350, 200 mM Zn Acetate, 0.1 M Imidazole Malate, 5% Glycerol, pH 8.0, VAPOR DIFFUSION, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.7455.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.178α = 90
b = 147.301β = 90
c = 75.473γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2007-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.33098.30.0620.062134.31282512617
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)
12.32.38900.30.33.32.7

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2DTQ, chain A2.330128251199461998.430.219280.216370.27541RANDOM43.32
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]
-3.830.962.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.844
r_dihedral_angle_4_deg20.037
r_dihedral_angle_3_deg17.124
r_dihedral_angle_1_deg6.172
r_scangle_it2.117
r_angle_refined_deg1.482
r_scbond_it1.312
r_mcangle_it0.773
r_mcbond_it0.502
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.844
r_dihedral_angle_4_deg20.037
r_dihedral_angle_3_deg17.124
r_dihedral_angle_1_deg6.172
r_scangle_it2.117
r_angle_refined_deg1.482
r_scbond_it1.312
r_mcangle_it0.773
r_mcbond_it0.502
r_nbtor_refined0.311
r_symmetry_vdw_refined0.267
r_nbd_refined0.202
r_xyhbond_nbd_refined0.168
r_symmetry_hbond_refined0.166
r_chiral_restr0.085
r_metal_ion_refined0.013
r_bond_refined_d0.012
r_gen_planes_refined0.005
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_refined
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 Atoms1675
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing