☰ Navigation Tabs
Crystal structure of HIV epitope-scaffold 4E10_1XIZA_S0_001_N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XIZ Computationally-derived model of the epitope-scaffold, based on 1XIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 DI-AMMONIUM PHOSPHATE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.211 α = 90 b = 81.975 β = 90 c = 94.219 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 IMAGE PLATE RIGAKU RAXIS IV++ Rigaku Varimax HR 2008-01-03 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 1.9 49.21 97.5 0.057 17.2 4.43 30053 22.3
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) 1.9 1.97 95.2 0.341 2.6 4.4 2886
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 1XIZ 1.9 31.5 26499 1420 90.63 0.22615 0.22324 0.2328 0.27917 0.2881 RANDOM 32.353
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] -0.4 0.07 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.211 r_dihedral_angle_4_deg 14.779 r_dihedral_angle_3_deg 12.843 r_dihedral_angle_1_deg 5.156 r_scangle_it 2.345 r_scbond_it 1.686 r_mcangle_it 1.173 r_angle_refined_deg 1.056 r_mcbond_it 0.763 r_angle_other_deg 0.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.211 r_dihedral_angle_4_deg 14.779 r_dihedral_angle_3_deg 12.843 r_dihedral_angle_1_deg 5.156 r_scangle_it 2.345 r_scbond_it 1.686 r_mcangle_it 1.173 r_angle_refined_deg 1.056 r_mcbond_it 0.763 r_angle_other_deg 0.743 r_symmetry_vdw_other 0.354 r_symmetry_hbond_refined 0.266 r_xyhbond_nbd_refined 0.218 r_nbd_other 0.208 r_nbd_refined 0.205 r_nbtor_refined 0.186 r_mcbond_other 0.179 r_nbtor_other 0.087 r_chiral_restr 0.061 r_symmetry_vdw_refined 0.053 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 2448 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 15
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling