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Crystal structure of an lmp2a-derived peptide bound to human class i mhc hla-a2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BD2 pdb entry 1BD2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 22% PEG 3350, 0.2M AMMONIUM IODIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.8 56.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.75 α = 90 b = 141.44 β = 90 c = 141.67 γ = 90
Symmetry Space Group P 21 21 21
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 2005-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.9 100 99.8 0.095 5.803 4.4 79598
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 0.485 1.5 4.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1BD2 1.9 39.11 79533 4014 99.7 0.209 0.208 0.239 0.237 RANDOM 22.06
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] -0.75 -0.22 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.585 r_dihedral_angle_4_deg 17.415 r_dihedral_angle_3_deg 11.934 r_dihedral_angle_1_deg 4.996 r_scangle_it 3.957 r_scbond_it 2.523 r_mcangle_it 1.76 r_angle_refined_deg 1.337 r_mcbond_it 1.055 r_symmetry_hbond_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.585 r_dihedral_angle_4_deg 17.415 r_dihedral_angle_3_deg 11.934 r_dihedral_angle_1_deg 4.996 r_scangle_it 3.957 r_scbond_it 2.523 r_mcangle_it 1.76 r_angle_refined_deg 1.337 r_mcbond_it 1.055 r_symmetry_hbond_refined 0.322 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.275 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6212 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement CNS refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling CNS phasing