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Crystal structure of MOR03929, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C7X 5C7X and 2GMF experimental model PDB 2GMF 5C7X and 2GMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.75 293 100 mM Tris, pH 8.75, 200 mM LiSO4, 25-28 % (w/v) PEG 3350, 28mg/mL protein
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.235 α = 90 b = 158.235 β = 90 c = 158.235 γ = 90
Symmetry Space Group I 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2011-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0015 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.06 111.89 98.9 0.091 27.58 21.6 40747
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.06 2.24 95.9 0.734 20.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5C7X and 2GMF 2.06 111.89 38872 1777 99.8 0.19135 0.18998 0.22179 0.2049 RANDOM 37.433
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.215 r_dihedral_angle_4_deg 14.266 r_dihedral_angle_3_deg 11.941 r_dihedral_angle_1_deg 6.497 r_scangle_it 4.234 r_scbond_it 3.264 r_mcangle_it 2.197 r_mcbond_it 1.741 r_angle_refined_deg 1.26 r_angle_other_deg 0.917
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.215 r_dihedral_angle_4_deg 14.266 r_dihedral_angle_3_deg 11.941 r_dihedral_angle_1_deg 6.497 r_scangle_it 4.234 r_scbond_it 3.264 r_mcangle_it 2.197 r_mcbond_it 1.741 r_angle_refined_deg 1.26 r_angle_other_deg 0.917 r_mcbond_other 0.39 r_symmetry_vdw_other 0.177 r_nbd_refined 0.169 r_nbtor_refined 0.159 r_nbd_other 0.152 r_symmetry_hbond_refined 0.15 r_symmetry_vdw_refined 0.135 r_xyhbond_nbd_refined 0.091 r_nbtor_other 0.075 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3978 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 5
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement MOLREP phasing