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Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope peptide corresponding to N-terminus of HIV-2 protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 292 protein concentration 14mg/ml, 0.05M tri-sodium citrate, 0.1M sodium phosphate,
27% PEG 3400, 0.2M ammonium sulfate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.85 33.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.184 α = 90 b = 56.413 β = 102.13 c = 88.304 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 2001-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 1.88 30 96.5 0.055 16.88 8.2 35996 34737 19.3
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) 1.88 1.99 77.6 0.595 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1JP5 1.89 19.79 2 32745 1621 95.8 0.1961 0.196 0.1985 0.239 0.2419 RANDOM 41.1
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] 1.48 6.35 -0.97 -0.51
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.2 c_scangle_it 5.46 c_improper_angle_d 4.07 c_mcangle_it 3.84 c_scbond_it 3.74 c_angle_deg 3.2 c_mcbond_it 2.8 c_bond_d 0.729
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3793 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement