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Crystal structure of engineered antibody fragment based on 3D5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KTR PDB entry 1KTR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 PEG 8000, magnesium acetate, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.8 67.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 266.637 α = 90 b = 266.637 β = 90 c = 266.637 γ = 90
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 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.1 154.303 99.6 0.124 0.124 13.5 5.6 28384 28384
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.27 100 0.342 0.342 2.1 5.6 4134
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 1KTR 3.1 154.3 28371 1439 99.54 0.1858 0.1831 0.194 0.2378 0.2131 RANDOM 69.6674
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 37.673 r_dihedral_angle_3_deg 23.12 r_dihedral_angle_4_deg 18.743 r_dihedral_angle_1_deg 8.268 r_scangle_it 2.295 r_angle_refined_deg 1.871 r_scbond_it 1.344 r_mcangle_it 0.93 r_mcbond_it 0.455 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.673 r_dihedral_angle_3_deg 23.12 r_dihedral_angle_4_deg 18.743 r_dihedral_angle_1_deg 8.268 r_scangle_it 2.295 r_angle_refined_deg 1.871 r_scbond_it 1.344 r_mcangle_it 0.93 r_mcbond_it 0.455 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7272 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XSCALE data scaling