5OD8

Crystal structure of the RA-associated mAb B2 (Fab fragment)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NCJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29320% (w/v) PEG3350, 0.2 M Na3citrate
Crystal Properties
Matthews coefficientSolvent content
2.6853.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.41α = 90
b = 41.9β = 108.37
c = 97.49γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.292.5394.90.0560.0510.98210.83.22579529.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2769.70.2580.2430.79132.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3ncj2.292.5224454129694.570.201950.199720.24254RANDOM42.519
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]
-0.261.33-0.750.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.781
r_dihedral_angle_4_deg20.111
r_dihedral_angle_3_deg13.486
r_dihedral_angle_1_deg6.834
r_long_range_B_refined4.878
r_long_range_B_other4.789
r_angle_refined_deg1.376
r_angle_other_deg0.906
r_mcangle_it0.904
r_mcangle_other0.904
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.781
r_dihedral_angle_4_deg20.111
r_dihedral_angle_3_deg13.486
r_dihedral_angle_1_deg6.834
r_long_range_B_refined4.878
r_long_range_B_other4.789
r_angle_refined_deg1.376
r_angle_other_deg0.906
r_mcangle_it0.904
r_mcangle_other0.904
r_scangle_other0.65
r_mcbond_it0.485
r_mcbond_other0.485
r_scbond_it0.343
r_scbond_other0.343
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3335
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing