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MHC Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With beta-2 Microglobulin and pBM8 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NAN PDB ENTRY 1NAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 14% PEG 10000, 100 MM MES PH 6.3
Crystal Properties Matthews coefficient Solvent content 2.7 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.146 α = 90 b = 90.461 β = 111.02 c = 89.032 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 IMAGE PLATE MARRESEARCH 2004-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.9 20 99.9 0.07 12.6 3.4 78205
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 1.9 2 100 0.35 3.4 3.3
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 1NAN 1.9 15 74179 3930 100 0.212 0.21 0.2266 0.251 0.2688 RANDOM 27.25
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] -1.2 -0.52 2.16 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.002 r_dihedral_angle_4_deg 19.365 r_dihedral_angle_3_deg 14.946 r_dihedral_angle_1_deg 5.859 r_scangle_it 2.386 r_scbond_it 1.473 r_angle_refined_deg 1.194 r_mcangle_it 1.117 r_mcbond_it 0.645 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.002 r_dihedral_angle_4_deg 19.365 r_dihedral_angle_3_deg 14.946 r_dihedral_angle_1_deg 5.859 r_scangle_it 2.386 r_scbond_it 1.473 r_angle_refined_deg 1.194 r_mcangle_it 1.117 r_mcbond_it 0.645 r_nbtor_refined 0.3 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 6306 Nucleic Acid Atoms Solvent Atoms 644 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing