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10mer Crystal Structure of chicken MHC class I haplotype B21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BEV PDB ENTRY 3BEV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 27% PEG 3350, 0.1M HEPES pH 7.0, 0.1M MgCl2, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.393 α = 90 b = 88.711 β = 80.01 c = 100.23 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 MARRESEARCH 2005-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97650 ESRF BM14
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 2.6 30 0.097 0.097 13.2 39205
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) 2.6 2.69 0.323 0.323 2.8 1560
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 3BEV 2.6 29.15 30179 1514 97.49 0.237 0.234 0.2329 0.295 0.2909 RANDOM 28.337
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] 3.59 1.67 -1.88 -2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.044 r_dihedral_angle_3_deg 18.94 r_dihedral_angle_4_deg 14.392 r_scangle_it 6.769 r_dihedral_angle_1_deg 6.424 r_scbond_it 5.332 r_mcangle_it 4.752 r_mcbond_it 3.684 r_mcbond_other 1.461 r_angle_refined_deg 1.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.044 r_dihedral_angle_3_deg 18.94 r_dihedral_angle_4_deg 14.392 r_scangle_it 6.769 r_dihedral_angle_1_deg 6.424 r_scbond_it 5.332 r_mcangle_it 4.752 r_mcbond_it 3.684 r_mcbond_other 1.461 r_angle_refined_deg 1.336 r_angle_other_deg 0.974 r_nbd_refined 0.213 r_symmetry_vdw_other 0.209 r_nbd_other 0.202 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.184 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.115 r_symmetry_vdw_refined 0.1 r_nbtor_other 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6104 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing