☰ Navigation Tabs
HLA-A24 in complex with HIV-1 Nef126-10(8I10F)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20%(w/v) PEG3350, 200mM sodium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.576 α = 90 b = 78.414 β = 90 c = 87.278 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 100 CCD RAYONIX MX225HE 2012-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.66 50 99.1 0.084 10.7 5.4 54184
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 1.66 1.72 97.5 0.425 3.9 5234
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 3vz4 1.66 50 54150 2743 99.08 0.1772 0.1746 0.175 0.2263 0.229 RANDOM 24.1641
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] 2.12 -0.8 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.742 r_sphericity_free 29.428 r_dihedral_angle_4_deg 14.094 r_sphericity_bonded 13.819 r_dihedral_angle_3_deg 13.188 r_dihedral_angle_1_deg 5.449 r_rigid_bond_restr 4.958 r_angle_refined_deg 1.064 r_chiral_restr 0.076 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.742 r_sphericity_free 29.428 r_dihedral_angle_4_deg 14.094 r_sphericity_bonded 13.819 r_dihedral_angle_3_deg 13.188 r_dihedral_angle_1_deg 5.449 r_rigid_bond_restr 4.958 r_angle_refined_deg 1.064 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3139 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOLREP phasing