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Crystal structure of HIV epitope-scaffold 4E10_D0_1IS1A_001_C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IS1 Computationally-derived model of the epitope-scaffold, based on 1IS1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 PEG 4000, Ca chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.66 α = 90 b = 75.36 β = 90 c = 79.61 γ = 90
Symmetry Space Group C 2 2 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 2008-06-04 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 32.64 98.3 0.052 18.6 4.53 8462 8462 27.7
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 2.07 89.9 0.185 4 2.66 755
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 1IS1 2 27.37 8032 8032 396 98.17 0.20697 0.20444 0.2179 0.25969 0.2719 RANDOM 30.398
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] -0.05 -0.05 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.408 r_dihedral_angle_4_deg 18.106 r_dihedral_angle_3_deg 13.319 r_dihedral_angle_1_deg 4.013 r_scangle_it 3.3 r_scbond_it 2.233 r_mcangle_it 1.403 r_angle_refined_deg 1.004 r_mcbond_it 0.938 r_angle_other_deg 0.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.408 r_dihedral_angle_4_deg 18.106 r_dihedral_angle_3_deg 13.319 r_dihedral_angle_1_deg 4.013 r_scangle_it 3.3 r_scbond_it 2.233 r_mcangle_it 1.403 r_angle_refined_deg 1.004 r_mcbond_it 0.938 r_angle_other_deg 0.841 r_symmetry_vdw_other 0.322 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.219 r_mcbond_other 0.214 r_xyhbond_nbd_refined 0.207 r_nbd_other 0.202 r_symmetry_hbond_refined 0.191 r_nbtor_refined 0.178 r_nbtor_other 0.087 r_chiral_restr 0.057 r_bond_refined_d 0.011 r_bond_other_d 0.004 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 907 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement d*TREK data reduction d*TREK data scaling