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Crystal structure of a therapeutic single chain antibody in complex with amphetamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GK2 PDB ENTRY 3GK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.8 287.1 1.15M sodium citrate, 0.28M imidazole-malate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 287.1K
Crystal Properties Matthews coefficient Solvent content 2.38 42.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.545 α = 90 b = 65.227 β = 98.7 c = 48.593 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 325 mm CCD 2009-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 2.38 50 93.3 0.093 0.04 24.9 4.4 7947
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 3GK2 2.38 48.03 7560 373 92.2 0.219 0.215 0.2138 0.293 0.2873 RANDOM 28.95
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] 2.89 0.24 -2.06 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.288 r_dihedral_angle_4_deg 20.575 r_dihedral_angle_3_deg 19.789 r_dihedral_angle_1_deg 7.111 r_scangle_it 3.333 r_scbond_it 2.186 r_angle_refined_deg 1.865 r_mcangle_it 1.588 r_mcbond_it 0.851 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.288 r_dihedral_angle_4_deg 20.575 r_dihedral_angle_3_deg 19.789 r_dihedral_angle_1_deg 7.111 r_scangle_it 3.333 r_scbond_it 2.186 r_angle_refined_deg 1.865 r_mcangle_it 1.588 r_mcbond_it 0.851 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 1778 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing