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Crystal structure of the Fab region of a neutralizing fully human antibody against GM-CSF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 2.0M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.46 54.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.12 α = 90 b = 66.69 β = 90 c = 129.04 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 CCD MARMOSAIC 225 mm CCD 2016-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPring-8 BL38B1
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 1.81 46.37 98.1 0.068 27.2 13.8 43756
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 1.81 1.85 0.171
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 4EOW 1.81 46.37 43716 2270 97.66 0.16272 0.16121 0.19133 0.213 RANDOM 19.529
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 35.03 r_dihedral_angle_4_deg 14.095 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_1_deg 8.642 r_long_range_B_refined 7.424 r_long_range_B_other 7.423 r_scangle_other 6.255 r_scbond_it 4.597 r_scbond_other 4.595 r_mcangle_other 3.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.03 r_dihedral_angle_4_deg 14.095 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_1_deg 8.642 r_long_range_B_refined 7.424 r_long_range_B_other 7.423 r_scangle_other 6.255 r_scbond_it 4.597 r_scbond_other 4.595 r_mcangle_other 3.463 r_mcangle_it 3.462 r_mcbond_it 2.781 r_mcbond_other 2.776 r_angle_refined_deg 0.796 r_angle_other_deg 0.523 r_chiral_restr 0.063 r_gen_planes_refined 0.019 r_bond_refined_d 0.005 r_gen_planes_other 0.002 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3301 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction pointless data scaling MOLREP phasing