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Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RZK YU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG experimental model PDB 412D YU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG experimental model PDB 1RZG YU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 17-19% polyethylene glycol (PEG) 1500, 0.1 M Na cacodylate pH 6.5, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.02 59.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.6 α = 90 b = 53.021 β = 104.64 c = 225.326 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 MARRESEARCH 2004-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 3.3 50 67.8 0.133 0.133 9.1 3.1 25816 -3
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 3.3 3.42 16.2 0.537 1.3 1.7 595
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT YU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG 3.3 20 38401 25600 1329 66.7 0.202 0.2063 0.269 0.2083 random 156
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] -46.386 -20.021 16.91 29.475
RMS Deviations Key Refinement Restraint Deviation f_angle_deg 1.092 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14497 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 490
Software Software Software Name Purpose PHENIX refinement AMoRE phasing CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling