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Crystal structure of the arthritogenic antibody M2139 (Fab fragment) in complex with the triple-helical J1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y5T PDB ENTRY 2Y5T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1.7 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7.0, 10 % DIOXANE
Crystal Properties Matthews coefficient Solvent content 4.02 69.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.18 α = 90 b = 95.18 β = 90 c = 190.42 γ = 120
Symmetry Space Group P 31 2 1
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 ADSC QUANTUM 210 2010-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 3.25 82.5 99.7 0.08 13.5 4.7 16327 2
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 3.25 3.43 99.4 0.64 2 4
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 PDB ENTRY 2Y5T 3.25 50 15468 823 99.62 0.22378 0.22175 0.221 0.2627 0.2586 RANDOM 117.469
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] 2.42 2.42 2.42 -7.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.777 r_dihedral_angle_4_deg 24.207 r_dihedral_angle_3_deg 18.317 r_long_range_B_refined 16.784 r_long_range_B_other 16.783 r_mcangle_it 10.886 r_mcangle_other 10.885 r_scangle_other 10.82 r_mcbond_it 7.076 r_mcbond_other 7.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.777 r_dihedral_angle_4_deg 24.207 r_dihedral_angle_3_deg 18.317 r_long_range_B_refined 16.784 r_long_range_B_other 16.783 r_mcangle_it 10.886 r_mcangle_other 10.885 r_scangle_other 10.82 r_mcbond_it 7.076 r_mcbond_other 7.064 r_dihedral_angle_1_deg 6.807 r_scbond_it 6.795 r_scbond_other 6.793 r_angle_other_deg 1.745 r_angle_refined_deg 1.556 r_chiral_restr 0.16 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3770 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing