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Crystal structure of MOR04302, 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 2GMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 100 mM sodium acetate, pH 4.0-4.3, 39-42 % (w/v) PEG 400, 35 mg/mL protein
Crystal Properties Matthews coefficient Solvent content 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.68 α = 90 b = 158.68 β = 90 c = 158.68 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 X06SA 1.0 SLS X06SA
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 2.25 112.2 99.9 0.074 30.33 24.9 31568
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 2.25 2.39 99.3 0.66 24.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2GMF 2.25 112.2 30163 1393 99.96 0.18132 0.17957 0.1862 0.21898 0.223 RANDOM 51.358
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.294 r_dihedral_angle_4_deg 14.815 r_dihedral_angle_3_deg 12.315 r_dihedral_angle_1_deg 6.727 r_scangle_it 5.007 r_scbond_it 3.913 r_mcangle_it 2.689 r_mcbond_it 2.062 r_angle_refined_deg 1.314 r_angle_other_deg 0.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.294 r_dihedral_angle_4_deg 14.815 r_dihedral_angle_3_deg 12.315 r_dihedral_angle_1_deg 6.727 r_scangle_it 5.007 r_scbond_it 3.913 r_mcangle_it 2.689 r_mcbond_it 2.062 r_angle_refined_deg 1.314 r_angle_other_deg 0.934 r_mcbond_other 0.492 r_symmetry_vdw_other 0.19 r_nbd_refined 0.173 r_nbtor_refined 0.162 r_nbd_other 0.157 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.109 r_symmetry_vdw_refined 0.077 r_chiral_restr 0.076 r_nbtor_other 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 3969 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 17
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement MOLREP phasing