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Structure based design of sub-nanomolar affinity anti-methamphetamine single chain antibodies.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GKZ PDB ENTRY 3GKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.25 287.15 0.917 M sodium citrate, pH 8.2, 0.324 M imidazole-malate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 287.15K
Crystal Properties Matthews coefficient Solvent content 2.02 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.516 α = 90 b = 65.265 β = 98.2 c = 48.483 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 Rh coated flat mirrors 2012-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.2 0.087 34.2 4.8 14299 14299
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 0.33 8.1 5.1
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 3GKZ 2 38.66 13554 719 99.03 0.19669 0.19369 0.1999 0.25361 0.2476 RANDOM 27.454
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] 0.06 -0.01 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.737 r_dihedral_angle_4_deg 21.744 r_dihedral_angle_3_deg 16.957 r_dihedral_angle_1_deg 7.461 r_scangle_it 4.36 r_scbond_it 3.148 r_mcangle_it 2.039 r_angle_refined_deg 1.987 r_mcbond_it 1.21 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.737 r_dihedral_angle_4_deg 21.744 r_dihedral_angle_3_deg 16.957 r_dihedral_angle_1_deg 7.461 r_scangle_it 4.36 r_scbond_it 3.148 r_mcangle_it 2.039 r_angle_refined_deg 1.987 r_mcbond_it 1.21 r_chiral_restr 0.135 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 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 1756 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 11
Software Software Software Name Purpose HKL-2000 data collection CCP4 model building REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing