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Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with UG29 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B0S PDB ENTRY 2B0S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 25% MPEG 5000, 0.2M disodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.899 α = 90 b = 94.501 β = 90 c = 96.617 γ = 90
Symmetry Space Group P 21 21 21
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 4 2003-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.00 ALS 5.0.1
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 67.42 99.9 0.069 19.7 4.8 39609 39609 -3 33.6
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 0.612 2.6 4.8 1963
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 (All) 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 2B0S 2 67.42 37576 37576 1982 99.78 0.20646 0.20646 0.20473 0.2135 0.23837 0.2428 RANDOM 35.055
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] -1.19 2.5 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.917 r_dihedral_angle_3_deg 15.336 r_dihedral_angle_4_deg 12.231 r_dihedral_angle_1_deg 7.348 r_scangle_it 3.235 r_scbond_it 2.38 r_angle_refined_deg 1.728 r_mcangle_it 1.495 r_mcbond_it 1.215 r_angle_other_deg 0.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.917 r_dihedral_angle_3_deg 15.336 r_dihedral_angle_4_deg 12.231 r_dihedral_angle_1_deg 7.348 r_scangle_it 3.235 r_scbond_it 2.38 r_angle_refined_deg 1.728 r_mcangle_it 1.495 r_mcbond_it 1.215 r_angle_other_deg 0.967 r_mcbond_other 0.27 r_symmetry_vdw_other 0.233 r_nbd_refined 0.218 r_nbd_other 0.198 r_symmetry_vdw_refined 0.186 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.117 r_symmetry_hbond_refined 0.099 r_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3449 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing CNS refinement DENZO data reduction