☰ Navigation Tabs
Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with UG1033 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 13.75% PEG 20000, 0.05M disodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.95 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.716 α = 90 b = 96.89 β = 90 c = 97.018 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 315 2003-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98397 SSRL BL11-1
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 2.348 31.31 98.6 0.057 31.9 3.7 24986 24986 -3 56
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 2.348 2.39 92.8 0.488 2.36 3.1 1118
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 2.348 31.31 23732 23732 1208 100 0.21287 0.21287 0.21118 0.2182 0.24446 0.252 RANDOM 59.833
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] -0.52 0.6 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.416 r_dihedral_angle_4_deg 15.236 r_dihedral_angle_3_deg 14.904 r_dihedral_angle_1_deg 6.726 r_scangle_it 1.83 r_angle_refined_deg 1.328 r_scbond_it 1.222 r_angle_other_deg 0.849 r_mcangle_it 0.739 r_mcbond_it 0.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.416 r_dihedral_angle_4_deg 15.236 r_dihedral_angle_3_deg 14.904 r_dihedral_angle_1_deg 6.726 r_scangle_it 1.83 r_angle_refined_deg 1.328 r_scbond_it 1.222 r_angle_other_deg 0.849 r_mcangle_it 0.739 r_mcbond_it 0.628 r_symmetry_vdw_other 0.246 r_nbd_refined 0.199 r_nbd_other 0.197 r_symmetry_vdw_refined 0.185 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.13 r_xyhbond_nbd_other 0.11 r_mcbond_other 0.099 r_nbtor_other 0.085 r_chiral_restr 0.079 r_symmetry_hbond_refined 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3440 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing CNS refinement DENZO data reduction