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Crystal structure of B*27:04 complex bound to the pVIPR peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 28%(w/v) PEG 8000, 100 mM Tris-HCl pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.7 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.77 α = 90 b = 82.16 β = 90 c = 109.863 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 ADSC QUANTUM 4 2005-02-03 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 1.6 20 99.5 0.045 29.1 4.9 61196 14.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 97.4 4.5 4.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2a83 1.6 20 58005 3098 99.52 0.1564 0.15542 0.17445 0.191 RANDOM 17.8
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] -0.6 -0.26 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.423 r_dihedral_angle_4_deg 17.075 r_dihedral_angle_3_deg 11.607 r_dihedral_angle_1_deg 6.012 r_scangle_it 3.572 r_scbond_it 2.239 r_angle_refined_deg 1.448 r_mcangle_it 1.411 r_angle_other_deg 0.86 r_mcbond_it 0.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.423 r_dihedral_angle_4_deg 17.075 r_dihedral_angle_3_deg 11.607 r_dihedral_angle_1_deg 6.012 r_scangle_it 3.572 r_scbond_it 2.239 r_angle_refined_deg 1.448 r_mcangle_it 1.411 r_angle_other_deg 0.86 r_mcbond_it 0.797 r_mcbond_other 0.237 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3188 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing