5D70

Crystal structure of MOR03929, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.75293100 mM Tris, pH 8.75, 200 mM LiSO4, 25-28 % (w/v) PEG 3350, 28mg/mL protein
Crystal Properties
Matthews coefficientSolvent content
2.5551.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.235α = 90
b = 158.235β = 90
c = 158.235γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-01-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0015SLSX06DA

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
12.06111.8998.90.09127.5821.640747
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)
12.062.2495.90.73420.1

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 REPLACEMENTTHROUGHOUT5C7X and 2GMF2.06111.8938872177799.80.191350.189980.22179RANDOM37.433
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.215
r_dihedral_angle_4_deg14.266
r_dihedral_angle_3_deg11.941
r_dihedral_angle_1_deg6.497
r_scangle_it4.234
r_scbond_it3.264
r_mcangle_it2.197
r_mcbond_it1.741
r_angle_refined_deg1.26
r_angle_other_deg0.917
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.215
r_dihedral_angle_4_deg14.266
r_dihedral_angle_3_deg11.941
r_dihedral_angle_1_deg6.497
r_scangle_it4.234
r_scbond_it3.264
r_mcangle_it2.197
r_mcbond_it1.741
r_angle_refined_deg1.26
r_angle_other_deg0.917
r_mcbond_other0.39
r_symmetry_vdw_other0.177
r_nbd_refined0.169
r_nbtor_refined0.159
r_nbd_other0.152
r_symmetry_hbond_refined0.15
r_symmetry_vdw_refined0.135
r_xyhbond_nbd_refined0.091
r_nbtor_other0.075
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
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 Atoms3978
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms5

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MOLREPphasing