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Mhc Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With beta-2 Microglobulin and pBM1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CLV PDB ENTRY 1CLV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 14% PEG 6000 ; 100 MM MES PH 6.3
Crystal Properties Matthews coefficient Solvent content 2.7 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.588 α = 90 b = 90.759 β = 111.35 c = 89.248 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 CCD ADSC CCD 2005-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.9 51.23 96.8 0.06 14.9 3.7 75377
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 86.8 0.38 3.3 3.5
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 1CLV 1.9 15 71423 3777 96.7 0.208 0.206 0.2185 0.247 0.2586 RANDOM 25.62
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] -0.88 -0.45 1.58 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.807 r_dihedral_angle_4_deg 20.086 r_dihedral_angle_3_deg 14.452 r_dihedral_angle_1_deg 5.609 r_scangle_it 2.484 r_scbond_it 1.534 r_angle_refined_deg 1.183 r_mcangle_it 1.156 r_mcbond_it 0.678 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.807 r_dihedral_angle_4_deg 20.086 r_dihedral_angle_3_deg 14.452 r_dihedral_angle_1_deg 5.609 r_scangle_it 2.484 r_scbond_it 1.534 r_angle_refined_deg 1.183 r_mcangle_it 1.156 r_mcbond_it 0.678 r_nbtor_refined 0.301 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.169 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.079 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 6298 Nucleic Acid Atoms Solvent Atoms 641 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CNS phasing