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crystal structure of class I MHC H-2Kk in complex with an octapeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LEG pdb entry 1LEG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 NaCl, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.38 71.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.758 α = 90 b = 111.758 β = 90 c = 109.417 γ = 120
Symmetry Space Group P 32 2 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 2003-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9763 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 15 99 0.087 0.069 8.9 2.7 27538 27403 1 1 51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.64 99.2 0.419 0.338 2.1 2.7 3935
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 (All) 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 1LEG 2.5 14.87 26053 1344 99.26 0.21202 0.21202 0.21 0.2814 0.25141 0.3118 RANDOM 27.161
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] 1.8 0.9 1.8 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.563 r_scangle_it 2.347 r_scbond_it 1.342 r_angle_refined_deg 1.157 r_mcangle_it 0.998 r_angle_other_deg 0.777 r_mcbond_it 0.516 r_symmetry_vdw_other 0.309 r_nbd_other 0.224 r_xyhbond_nbd_refined 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.563 r_scangle_it 2.347 r_scbond_it 1.342 r_angle_refined_deg 1.157 r_mcangle_it 0.998 r_angle_other_deg 0.777 r_mcbond_it 0.516 r_symmetry_vdw_other 0.309 r_nbd_other 0.224 r_xyhbond_nbd_refined 0.2 r_nbd_refined 0.178 r_symmetry_hbond_refined 0.12 r_symmetry_vdw_refined 0.087 r_nbtor_other 0.082 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3132 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling AMoRE phasing