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Crystal structure of hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing the 4e10 epitope on gp41
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TZG PBD ENTRY 1TZG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20% PEG 3350, 0.2 M ammonium nitrate, pH no buffer, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.31 46.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.425 α = 90 b = 111.498 β = 106.44 c = 79.379 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 MARMOSAIC 325 mm CCD 2005-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.95369 SSRL BL9-2
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 2.1 50 99.3 0.094 14.1 3.7 51978 51614 3 31.6
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) 2.1 2.15 99 0.324 2.7 3.7 3779
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 PBD ENTRY 1TZG 2.1 50 51990 51545 2560 99.1 0.236 0.2345 0.271 0.2229 RANDOM 34.7
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] 9.568 0.928 -8.225 -1.343
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.952 c_mcangle_it 2.282 c_scbond_it 2.043 c_mcbond_it 1.433 c_angle_deg 1.4 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6916 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing CNS refinement HKL-2000 data reduction