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Crystal structure of HIV epitope-scaffold 4E10_D0_1ISEA_004_N 4E10 Fv complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TZG Computationally-derived model of the epitope-scaffold Fv complex, with the Fv based on PDB ID 1TZG.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 PEG 2000 MME, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.977 α = 90 b = 88.623 β = 90 c = 149.997 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 107 CCD RIGAKU SATURN 944+ Rigaku Varimax HF 2008-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 29.54 96.2 0.102 7.1 3.45 19356 19356 69.7
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) 2.7 2.8 85.5 0.405 2.2 2.86 1705
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-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 epitope-scaffold Fv complex, with the Fv based on PDB ID 1TZG. 2.7 28.99 19284 19284 980 96.02 0.24732 0.24267 0.2482 0.33503 0.3341 RANDOM 41.289
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] -0.09 -0.16 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.397 r_dihedral_angle_3_deg 18.403 r_dihedral_angle_4_deg 14.274 r_dihedral_angle_1_deg 5.924 r_scangle_it 1.435 r_angle_refined_deg 1.132 r_scbond_it 0.956 r_angle_other_deg 0.806 r_mcangle_it 0.747 r_mcbond_it 0.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.397 r_dihedral_angle_3_deg 18.403 r_dihedral_angle_4_deg 14.274 r_dihedral_angle_1_deg 5.924 r_scangle_it 1.435 r_angle_refined_deg 1.132 r_scbond_it 0.956 r_angle_other_deg 0.806 r_mcangle_it 0.747 r_mcbond_it 0.541 r_nbd_refined 0.213 r_nbd_other 0.195 r_symmetry_vdw_other 0.192 r_symmetry_vdw_refined 0.187 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.104 r_nbtor_other 0.084 r_chiral_restr 0.051 r_mcbond_other 0.05 r_bond_refined_d 0.009 r_bond_other_d 0.007 r_xyhbond_nbd_other 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5112 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 4
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling