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1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 K/Na-Phosphate, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.02 59.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.549 α = 90 b = 87.65 β = 90 c = 45.118 γ = 90
Symmetry Space Group P 21 21 2
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 Flat mirror (vertical focusing) 2000-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.970 SSRL BL9-1
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 1.35 30 98.9 0.053 23.95 3.4 117515 16.5
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 1.35 1.37 95.3 0.813 1.13 2.5 5606
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.35 18.35 109986 104434 5552 93.64 0.15023 0.14949 0.2337 0.1639 0.2435 RANDOM 9.96
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] -0.26 0.44 -0.18
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 20.989 r_dihedral_angle_2_deg 16.934 r_dihedral_angle_1_deg 5.638 r_scangle_it 4.043 r_sphericity_bonded 3.587 r_scbond_it 2.755 r_mcangle_it 1.691 r_angle_refined_deg 1.608 r_angle_other_deg 1.19 r_rigid_bond_restr 1.163
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 20.989 r_dihedral_angle_2_deg 16.934 r_dihedral_angle_1_deg 5.638 r_scangle_it 4.043 r_sphericity_bonded 3.587 r_scbond_it 2.755 r_mcangle_it 1.691 r_angle_refined_deg 1.608 r_angle_other_deg 1.19 r_rigid_bond_restr 1.163 r_mcbond_it 1.124 r_nbtor_other 0.566 r_symmetry_hbond_refined 0.222 r_nbd_refined 0.218 r_nbd_other 0.201 r_symmetry_vdw_other 0.196 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.166 r_symmetry_hbond_other 0.128 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3119 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing