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Crystal structure of HIV epitope-scaffold 4E10 Fv complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TZG computationally-derived model of the Fv, based on 1TZG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 0.2 M calcium acetate, 8% PEG 8000, 0.1 M Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.24 45.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.4 α = 90 b = 92.4 β = 90 c = 272.79 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 107 IMAGE PLATE RIGAKU RAXIS IV Rigaku VariMax HR 2008-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.7 69.02 98.6 0.104 7.5 4.56 19557 19557 63.6
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 2.7 2.8 99.6 0.347 2.9 4.29 8305
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT computationally-derived model of the Fv, based on 1TZG 2.7 60.08 18347 953 97.3 0.23171 0.2289 0.2319 0.28697 0.2859 RANDOM 59.2
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.999 r_dihedral_angle_4_deg 19.868 r_dihedral_angle_3_deg 16.597 r_dihedral_angle_1_deg 5.646 r_scangle_it 2.421 r_scbond_it 1.611 r_angle_refined_deg 1.109 r_mcangle_it 1.048 r_angle_other_deg 0.722 r_mcbond_it 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.999 r_dihedral_angle_4_deg 19.868 r_dihedral_angle_3_deg 16.597 r_dihedral_angle_1_deg 5.646 r_scangle_it 2.421 r_scbond_it 1.611 r_angle_refined_deg 1.109 r_mcangle_it 1.048 r_angle_other_deg 0.722 r_mcbond_it 0.7 r_symmetry_vdw_other 0.242 r_nbd_refined 0.236 r_nbd_other 0.227 r_symmetry_vdw_refined 0.2 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_other 0.122 r_mcbond_other 0.094 r_nbtor_other 0.088 r_metal_ion_refined 0.077 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_bond_other_d 0.007 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3794 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 1
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling