☰ Navigation Tabs
Crystal Structure of the Fab Fragment of a Glycosylated Lymphoma Antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 25 %w/v Polyethylene Glycol 3350
0.200 M Magnesium Chloride
0.100 M bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.34 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.33 α = 90 b = 60.79 β = 90 c = 84.17 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER2 XE 16M 2018-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 50.61 100 0.082 0.99 13.8 6.4 57128
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 100 0.49 1 6.4
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 5NIV 1.65 50.61 54318 2765 99.97 0.17622 0.1747 0.1837 0.20605 0.2118 RANDOM 25.273
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] 0.59 0.33 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.434 r_dihedral_angle_4_deg 16.568 r_dihedral_angle_1_deg 16.225 r_dihedral_angle_3_deg 11.939 r_long_range_B_refined 4.91 r_long_range_B_other 4.625 r_scangle_other 2.358 r_mcangle_it 1.815 r_mcangle_other 1.815 r_scbond_it 1.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.434 r_dihedral_angle_4_deg 16.568 r_dihedral_angle_1_deg 16.225 r_dihedral_angle_3_deg 11.939 r_long_range_B_refined 4.91 r_long_range_B_other 4.625 r_scangle_other 2.358 r_mcangle_it 1.815 r_mcangle_other 1.815 r_scbond_it 1.462 r_scbond_other 1.462 r_angle_refined_deg 1.461 r_angle_other_deg 1.346 r_mcbond_it 1.099 r_mcbond_other 1.096 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 3386 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing