5D71

Crystal structure of MOR04302, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GMF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.2293100 mM sodium acetate, pH 4.0-4.3, 39-42 % (w/v) PEG 400, 35 mg/mL protein
Crystal Properties
Matthews coefficientSolvent content
2.5752.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.68α = 90
b = 158.68β = 90
c = 158.68γ = 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 X06SA1.0SLSX06SA

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
12.25112.299.90.07430.3324.931568
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)
12.252.3999.30.6624.3

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 REPLACEMENTTHROUGHOUT2GMF2.25112.230163139399.960.181320.179570.21898RANDOM51.358
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_deg34.294
r_dihedral_angle_4_deg14.815
r_dihedral_angle_3_deg12.315
r_dihedral_angle_1_deg6.727
r_scangle_it5.007
r_scbond_it3.913
r_mcangle_it2.689
r_mcbond_it2.062
r_angle_refined_deg1.314
r_angle_other_deg0.934
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.294
r_dihedral_angle_4_deg14.815
r_dihedral_angle_3_deg12.315
r_dihedral_angle_1_deg6.727
r_scangle_it5.007
r_scbond_it3.913
r_mcangle_it2.689
r_mcbond_it2.062
r_angle_refined_deg1.314
r_angle_other_deg0.934
r_mcbond_other0.492
r_symmetry_vdw_other0.19
r_nbd_refined0.173
r_nbtor_refined0.162
r_nbd_other0.157
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.109
r_symmetry_vdw_refined0.077
r_chiral_restr0.076
r_nbtor_other0.076
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3969
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms17

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MOLREPphasing