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Crystal structure of HIV epitope-scaffold 4E10_1VI7A_S0_002_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 Na acetate, imidazole, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.06 59.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.85 α = 90 b = 145.95 β = 92.43 c = 78.55 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 107 CCD RIGAKU SATURN 944+ Rigaku Varimax HF 2008-10-22 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 2.65 28.01 98.9 0.095 9.4 3.88 49017 49017 62.3
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) 2.65 2.74 98.6 0.376 2.7 3.68 4883
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. 2.65 26.7 48955 48955 2478 98.53 0.22426 0.22173 0.2308 0.27023 0.2747 RANDOM 47.111
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.776 r_dihedral_angle_4_deg 17.741 r_dihedral_angle_3_deg 15.617 r_dihedral_angle_1_deg 5.13 r_scangle_it 1.696 r_mcangle_it 1.052 r_scbond_it 1.039 r_angle_refined_deg 0.927 r_angle_other_deg 0.643 r_mcbond_it 0.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.776 r_dihedral_angle_4_deg 17.741 r_dihedral_angle_3_deg 15.617 r_dihedral_angle_1_deg 5.13 r_scangle_it 1.696 r_mcangle_it 1.052 r_scbond_it 1.039 r_angle_refined_deg 0.927 r_angle_other_deg 0.643 r_mcbond_it 0.585 r_symmetry_vdw_other 0.23 r_nbd_refined 0.208 r_nbd_other 0.208 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.188 r_symmetry_hbond_refined 0.161 r_symmetry_vdw_refined 0.132 r_xyhbond_nbd_other 0.101 r_nbtor_other 0.089 r_mcbond_other 0.067 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 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 8997 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling