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Crystal structure of anti-HIV-1 Fab 268-D in complex with V3 peptide MN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U6A PDB entry 1U6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 296.15 30% PEG 8000, 0.2M Ammonium Acetate, 0.1M Sodium Cacodylate pH 6.5, vapor diffusion, hanging drop, temperature 296.15K
Crystal Properties Matthews coefficient Solvent content 2.38 48.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.377 α = 90 b = 69.26 β = 107.24 c = 71.693 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 MAR CCD 165 mm mirrors 2008-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C
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 1.88 30.6 84.6 0.212 0.212 3.6 34455
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) 1.88 1.95 19.4 0.495 0.378 0.742 1.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1U6A 1.89 27.1 25909 32721 1734 98.95 0.19222 0.19115 0.1918 0.21261 0.2153 RANDOM 27.104
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 33.172 r_dihedral_angle_4_deg 12.546 r_dihedral_angle_3_deg 10.952 r_dihedral_angle_1_deg 5.891 r_scangle_it 1.441 r_angle_refined_deg 0.967 r_scbond_it 0.826 r_mcangle_it 0.661 r_mcbond_it 0.345 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.172 r_dihedral_angle_4_deg 12.546 r_dihedral_angle_3_deg 10.952 r_dihedral_angle_1_deg 5.891 r_scangle_it 1.441 r_angle_refined_deg 0.967 r_scbond_it 0.826 r_mcangle_it 0.661 r_mcbond_it 0.345 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3359 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing DENZO data reduction