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Crystal structure of MOR04357, 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, 40 mg/mL protein
Crystal Properties Matthews coefficient Solvent content 2.53 51.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.602 α = 90 b = 97.493 β = 90 c = 192.512 γ = 90
Symmetry Space Group P 21 21 21
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 2.95 96.26 94.5 0.18 6.8 4.7 29123
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 2.95 3.18 95.5 0.437 1.8 4.7
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 2.95 96.26 26834 593 94.18 0.23449 0.23353 0.2221 0.27613 0.2662 RANDOM 43.91
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] -5.15 10.2 -5.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.675 r_dihedral_angle_4_deg 15.602 r_dihedral_angle_3_deg 13.774 r_dihedral_angle_1_deg 6.466 r_scangle_it 3.06 r_scbond_it 2.032 r_mcangle_it 1.621 r_mcbond_it 1.315 r_angle_refined_deg 1.166 r_angle_other_deg 0.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.675 r_dihedral_angle_4_deg 15.602 r_dihedral_angle_3_deg 13.774 r_dihedral_angle_1_deg 6.466 r_scangle_it 3.06 r_scbond_it 2.032 r_mcangle_it 1.621 r_mcbond_it 1.315 r_angle_refined_deg 1.166 r_angle_other_deg 0.895 r_mcbond_other 0.17 r_nbtor_refined 0.158 r_nbd_refined 0.149 r_nbd_other 0.137 r_symmetry_vdw_refined 0.111 r_symmetry_vdw_other 0.104 r_xyhbond_nbd_refined 0.091 r_symmetry_hbond_refined 0.079 r_nbtor_other 0.073 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 8091 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 59
Software Software Software Name Purpose XDS data reduction SCALA data scaling REFMAC refinement MOLREP phasing