4HAF

Crystal structure of fc-fragment of human IgG2 antibody (primitive crystal form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AVEPDB entry 3ave

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M MES, 9% PEG 4000, 0.2 M AMMONIUM CHLORIDE, 5% MPD CRYO CONDITIONS: 0.1 M MES, 12% PEG 4000, 0.2 M AMMONIUM CHLORIDE, 20% PEG 400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.754.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.5α = 90
b = 75.17β = 90
c = 146.01γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944VARIMAX HF2010-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.0427.798.70.08518.76.73516235162-3-326.8
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)
12.042.0983.90.3573.12.6

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 REPLACEMENTTHROUGHOUTPDB entry 3ave2.04153409734097970960.200410.200410.199020.24819RANDOM35.1
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]
-0.69-0.240.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.759
r_scangle_it30.36
r_scbond_it27.505
r_dihedral_angle_4_deg15.524
r_dihedral_angle_3_deg14.008
r_dihedral_angle_1_deg5.794
r_mcangle_it5.104
r_mcbond_it3.233
r_angle_refined_deg1.189
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.759
r_scangle_it30.36
r_scbond_it27.505
r_dihedral_angle_4_deg15.524
r_dihedral_angle_3_deg14.008
r_dihedral_angle_1_deg5.794
r_mcangle_it5.104
r_mcbond_it3.233
r_angle_refined_deg1.189
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3183
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms99

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling