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HIV-1 neutralizing antibody Z13e1 in complex with epitope display protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FN0 PDB entry 3fn0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 19% PEG 4000, 10% isopropanol, 0.1M hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.623 α = 90 b = 99.216 β = 90 c = 105.533 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 MARMOSAIC 300 mm CCD 2009-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.058 APS 23-ID-B
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 2.15 49.63 99.9 0.117 16 4.9 33242 33242 -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 3fn0 2.15 49.63 31381 31381 1639 99.84 0.20984 0.2072 0.2414 0.26024 0.2534 RANDOM 45.892
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] 0.17 -0.16 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.455 r_dihedral_angle_4_deg 19.714 r_dihedral_angle_3_deg 15.938 r_dihedral_angle_1_deg 7.434 r_scangle_it 2.451 r_angle_refined_deg 1.701 r_scbond_it 1.692 r_angle_other_deg 1.074 r_mcangle_it 0.99 r_mcbond_it 0.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.455 r_dihedral_angle_4_deg 19.714 r_dihedral_angle_3_deg 15.938 r_dihedral_angle_1_deg 7.434 r_scangle_it 2.451 r_angle_refined_deg 1.701 r_scbond_it 1.692 r_angle_other_deg 1.074 r_mcangle_it 0.99 r_mcbond_it 0.574 r_mcbond_other 0.176 r_chiral_restr 0.097 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4116 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 68
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling