☰ Navigation Tabs
Crystal structure of human IgG ABT-325 Fab Fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FNS PDB ENTRY 1FNS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10.5 277 ABT-325 FAB FRAGMENT (20 MG/ML, 2 MICROLITERS [UL]) WAS MIXED WITH 2 UL OF A RESERVOIR SOLUTION CONSISTING OF 25 TO 30% POLYETHYLENEGLYCOL (PEG) 400, 100 MM CAPS, PH 10.5 AND SUSPENDED OVER THE RESERVOIR AT 277 K. ROD-LIKE CRYSTALS APPEARED WITHIN ONE DAY.
Crystal Properties Matthews coefficient Solvent content 2.7 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.406 α = 90 b = 74.069 β = 90 c = 107.271 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 MARRESEARCH MIRRORS 2003-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID APS 32-ID
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 1.49 50 99 0.08 9.8 6.4 83126 2 16
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 1.49 1.54 92.3 0.41 3.1 4.1
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 PDB ENTRY 1FNS 1.49 30.71 78910 4138 98.9 0.155 0.153 0.1644 0.179 0.1885 RANDOM 13.17
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] -0.22 0.09 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.475 r_dihedral_angle_4_deg 23.278 r_dihedral_angle_3_deg 11.577 r_dihedral_angle_1_deg 6.478 r_scangle_it 3.533 r_scbond_it 2.601 r_angle_refined_deg 1.569 r_mcangle_it 1.504 r_mcbond_it 1.257 r_angle_other_deg 0.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.475 r_dihedral_angle_4_deg 23.278 r_dihedral_angle_3_deg 11.577 r_dihedral_angle_1_deg 6.478 r_scangle_it 3.533 r_scbond_it 2.601 r_angle_refined_deg 1.569 r_mcangle_it 1.504 r_mcbond_it 1.257 r_angle_other_deg 0.903 r_symmetry_vdw_other 0.232 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.197 r_nbd_other 0.197 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.096 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 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_mcbond_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 3333 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing