5ODB

Crystal structure of the RA-associated mAb D10 (chimeric Fab fragment)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZUQ2zuq, 2dag
experimental modelPDB 2DAG2zuq, 2dag

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.752932.55 M ammonium sulfate, 0.1 M citrate pH 4.75, 0.1 M NDSB-256
Crystal Properties
Matthews coefficientSolvent content
2.2143.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.368α = 90
b = 66.714β = 93.85
c = 72.764γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.07201ESRFID29

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
11.5347.2699.10.0380.0370.99513.92.86753913.2
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)
11.531.5699.70.3890.3670.7212.32.8

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 REPLACEMENTTHROUGHOUT2zuq, 2dag1.5347.2664026340898.80.188850.187520.21387RANDOM19.706
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]
-0.580.53-0.090.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.201
r_dihedral_angle_4_deg14.032
r_dihedral_angle_3_deg10.638
r_dihedral_angle_1_deg6.649
r_long_range_B_other4.665
r_long_range_B_refined4.663
r_scangle_other2.508
r_mcangle_it2.126
r_mcangle_other2.125
r_scbond_it1.581
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.201
r_dihedral_angle_4_deg14.032
r_dihedral_angle_3_deg10.638
r_dihedral_angle_1_deg6.649
r_long_range_B_other4.665
r_long_range_B_refined4.663
r_scangle_other2.508
r_mcangle_it2.126
r_mcangle_other2.125
r_scbond_it1.581
r_scbond_other1.581
r_angle_refined_deg1.471
r_mcbond_other1.274
r_mcbond_it1.273
r_angle_other_deg0.929
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms3213
Nucleic Acid Atoms
Solvent Atoms448
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing