☰ Navigation Tabs
Crystal structure of the RA-associated mAb B2 (Fab fragment)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NCJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% (w/v) PEG3350, 0.2 M Na3citrate
Crystal Properties Matthews coefficient Solvent content 2.68 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.41 α = 90 b = 41.9 β = 108.37 c = 97.49 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS 6M-F 2013-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.2 92.53 94.9 0.056 0.051 0.982 10.8 3.2 25795 29.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 69.7 0.258 0.243 0.791 3 2.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ncj 2.2 92.52 24454 1296 94.57 0.20195 0.19972 0.2057 0.24254 0.2478 RANDOM 42.519
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] -0.26 1.33 -0.75 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.781 r_dihedral_angle_4_deg 20.111 r_dihedral_angle_3_deg 13.486 r_dihedral_angle_1_deg 6.834 r_long_range_B_refined 4.878 r_long_range_B_other 4.789 r_angle_refined_deg 1.376 r_angle_other_deg 0.906 r_mcangle_it 0.904 r_mcangle_other 0.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.781 r_dihedral_angle_4_deg 20.111 r_dihedral_angle_3_deg 13.486 r_dihedral_angle_1_deg 6.834 r_long_range_B_refined 4.878 r_long_range_B_other 4.789 r_angle_refined_deg 1.376 r_angle_other_deg 0.906 r_mcangle_it 0.904 r_mcangle_other 0.904 r_scangle_other 0.65 r_mcbond_it 0.485 r_mcbond_other 0.485 r_scbond_it 0.343 r_scbond_other 0.343 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 3335 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing