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Crystal structure of HIV epitope-scaffold 4E10_S0_1EZ3A_002_C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EZ3 Computationally-derived model of the epitope-scaffold, based on 1EZ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 Ammonium sulfate, bis Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.78 74.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.6 α = 90 b = 94.87 β = 90 c = 108.39 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 2008-05-09 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 2.5 28.82 99.5 0.107 6.6 4.53 33220 33220 66.7
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) 2.5 2.59 96.8 0.429 2 3.78 3180
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, based on 1EZ3 2.5 28.82 33123 33123 1672 99.39 0.25923 0.25702 0.2672 0.30121 0.3109 RANDOM 38.599
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] 0.06 -0.04 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.867 r_dihedral_angle_4_deg 21.723 r_dihedral_angle_3_deg 17.272 r_scangle_it 4.297 r_dihedral_angle_1_deg 3.952 r_scbond_it 2.96 r_mcbond_it 1.683 r_mcangle_it 1.667 r_angle_refined_deg 1.189 r_angle_other_deg 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.867 r_dihedral_angle_4_deg 21.723 r_dihedral_angle_3_deg 17.272 r_scangle_it 4.297 r_dihedral_angle_1_deg 3.952 r_scbond_it 2.96 r_mcbond_it 1.683 r_mcangle_it 1.667 r_angle_refined_deg 1.189 r_angle_other_deg 0.73 r_symmetry_vdw_other 0.357 r_nbd_refined 0.246 r_mcbond_other 0.222 r_symmetry_hbond_refined 0.199 r_nbtor_refined 0.198 r_nbd_other 0.194 r_xyhbond_nbd_refined 0.186 r_symmetry_vdw_refined 0.153 r_nbtor_other 0.089 r_chiral_restr 0.062 r_bond_refined_d 0.014 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_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 3096 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 55
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling