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Crystal structure of anti-HIV-1 antibody F240 Fab in complex with gp41 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 294 25% PEG 3350, 15% Isopropanol, 0.2M Ammonium citrate pH4.5
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.317 α = 90 b = 60.488 β = 94.13 c = 169.228 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 ADSC QUANTUM 315 RH coated flat mirror 2013-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.9753 SSRL BL7-1
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 2.54 168.79 98.8 0.158 9.4 2.9 33289 33289
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 2.54 2.58 98.6 0.957 1.4 2.9
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 3TNN 2.54 168.79 30876 1649 98.04 0.20649 0.20369 0.2064 0.2585 0.2593 RANDOM 43.223
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] -0.09 -0.15 -0.71 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.485 r_dihedral_angle_3_deg 15.719 r_dihedral_angle_4_deg 15.705 r_dihedral_angle_1_deg 7.157 r_long_range_B_refined 3.944 r_long_range_B_other 3.937 r_mcangle_it 1.616 r_mcangle_other 1.616 r_scangle_other 1.404 r_angle_refined_deg 1.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.485 r_dihedral_angle_3_deg 15.719 r_dihedral_angle_4_deg 15.705 r_dihedral_angle_1_deg 7.157 r_long_range_B_refined 3.944 r_long_range_B_other 3.937 r_mcangle_it 1.616 r_mcangle_other 1.616 r_scangle_other 1.404 r_angle_refined_deg 1.397 r_angle_other_deg 0.968 r_mcbond_it 0.9 r_mcbond_other 0.9 r_scbond_it 0.8 r_scbond_other 0.8 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 7031 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing