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Crystal structure of HIV epitope-scaffold 4E10_S0_1Z6NA_001
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z6N Computationally-derived model of the epitope-scaffold, based on 1Z6N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 Na/K tartrate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.85 68.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.41 α = 90 b = 56.41 β = 90 c = 324.13 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 2007-04-17 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 2.3 48.3 93.7 0.086 9 8.4 13770 13770 56.3
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) 2.3 2.38 91.5 0.373 3.9 6.83 1304
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 epitope-scaffold, based on 1Z6N 2.3 46.78 13064 667 93.47 0.25978 0.25831 0.3098 0.29042 0.329 RANDOM 49.573
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] -0.22 -0.11 -0.22 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.951 r_dihedral_angle_4_deg 19.905 r_dihedral_angle_3_deg 16.259 r_dihedral_angle_1_deg 4.95 r_scangle_it 2.547 r_scbond_it 1.662 r_angle_refined_deg 1.146 r_mcangle_it 1.035 r_angle_other_deg 0.781 r_mcbond_it 0.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.951 r_dihedral_angle_4_deg 19.905 r_dihedral_angle_3_deg 16.259 r_dihedral_angle_1_deg 4.95 r_scangle_it 2.547 r_scbond_it 1.662 r_angle_refined_deg 1.146 r_mcangle_it 1.035 r_angle_other_deg 0.781 r_mcbond_it 0.666 r_symmetry_vdw_other 0.214 r_nbd_refined 0.203 r_nbd_other 0.203 r_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.178 r_mcbond_other 0.133 r_symmetry_vdw_refined 0.098 r_nbtor_other 0.091 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1261 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 4
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling