☰ Navigation Tabs
Crystal structure of HLA-B*2705 complexed with a peptide derived from the human voltage-dependent calcium channel alpha1 subunit (residues 513-521)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A83 PDB ENTRY 2A83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 20%(w/v) PEG 8000, 150mM NaCl, 20mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.29 α = 90 b = 54.614 β = 99.33 c = 69.834 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 4 2004-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.94 20 0.113 16.2 18393 31104
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.97 0.36 4.8 1529
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 PDB ENTRY 2A83 1.94 19.46 28960 1544 98.12 0.17802 0.17553 0.175 0.22435 0.2255 RANDOM 27.115
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] 0.15 0.37 -0.06 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.015 r_dihedral_angle_3_deg 13.98 r_dihedral_angle_4_deg 13.565 r_dihedral_angle_1_deg 5.754 r_scangle_it 3.208 r_scbond_it 1.915 r_angle_refined_deg 1.259 r_mcangle_it 1.224 r_mcbond_it 0.642 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.015 r_dihedral_angle_3_deg 13.98 r_dihedral_angle_4_deg 13.565 r_dihedral_angle_1_deg 5.754 r_scangle_it 3.208 r_scbond_it 1.915 r_angle_refined_deg 1.259 r_mcangle_it 1.224 r_mcbond_it 0.642 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3187 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 18
Software Software Software Name Purpose DNA data collection EPMR phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling