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Crystal Structure Of HLA-B*2709 Complexed With the self-Peptide TIS from EGF-response factor 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W0V PDB ENTRY 1W0V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 20% PEG8000, 0.1M TRIS PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.7 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.175 α = 90 b = 82.67 β = 90 c = 110.177 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 IMAGE PLATE MARRESEARCH MIRRORS 2002-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
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 2.11 28.1 87 0.103 10 2.6 22935
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 2.11 2.18 86 0.32 2 2.4
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 1W0V 2.11 65.94 22935 1224 87.1 0.186 0.182 0.1862 0.245 0.2341 RANDOM 24.84
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] -0.32 -0.21 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.262 r_scangle_it 2.822 r_scbond_it 1.666 r_angle_refined_deg 1.238 r_mcangle_it 1.117 r_angle_other_deg 1.112 r_mcbond_it 0.589 r_symmetry_vdw_other 0.318 r_nbd_other 0.251 r_symmetry_hbond_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.262 r_scangle_it 2.822 r_scbond_it 1.666 r_angle_refined_deg 1.238 r_mcangle_it 1.117 r_angle_other_deg 1.112 r_mcbond_it 0.589 r_symmetry_vdw_other 0.318 r_nbd_other 0.251 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.162 r_symmetry_vdw_refined 0.11 r_chiral_restr 0.08 r_nbtor_other 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 3173 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL data reduction SCALEPACK data scaling MOLREP phasing