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Structure of an HIV epitope scaffold in complex with neutralizing antibody b12 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BOD pdb entries 2BOD, 2NY7 experimental model PDB 2NY7 pdb entries 2BOD, 2NY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 18% PEG-3350, 0.22M potassium nitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.453 α = 90 b = 93.097 β = 90 c = 94.373 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 CCD ADSC QUANTUM 4 2010-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0000 ALS 5.0.1
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 2.07 50 99.7 0.103 12.7 5.8 49114
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 2.07 2.11 95.3 0.34 5.2 2311
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entries 2BOD, 2NY7 2.07 45.23 48971 2485 99.25 0.1696 0.1678 0.2026 0.2211 RANDOM 40.2672
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] 0.06 -0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.898 r_dihedral_angle_4_deg 20.392 r_dihedral_angle_3_deg 12.588 r_dihedral_angle_1_deg 5.906 r_scangle_it 3.12 r_scbond_it 2.021 r_mcangle_it 1.33 r_angle_refined_deg 1.166 r_angle_other_deg 0.805 r_mcbond_it 0.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.898 r_dihedral_angle_4_deg 20.392 r_dihedral_angle_3_deg 12.588 r_dihedral_angle_1_deg 5.906 r_scangle_it 3.12 r_scbond_it 2.021 r_mcangle_it 1.33 r_angle_refined_deg 1.166 r_angle_other_deg 0.805 r_mcbond_it 0.718 r_mcbond_other 0.17 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5372 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction