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The structure of HLA-DRA, DRB3*0101 (DR52a) with bound platelet integrin peptide associated with fetal and neonatal alloimmune thrombocytopenia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLH PDB entry 1DLH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 297 10-20% PEG 8000, 0.1M sodium acetate, 10% (v/v) glycerol, 0.01M Cd2+, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K
Crystal Properties Matthews coefficient Solvent content 2.96 58.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.169 α = 90 b = 92.169 β = 90 c = 248.555 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 CCD ADSC QUANTUM 4 2002-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 2.25 30 94 0.12 15.8 51116 48049 2 2 42.9
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) 2.25 2.308 55.7 0.36 3.04
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1DLH 2.25 20.05 2 47777 44561 3684 93.27 0.214 0.20984 0.2064 0.26543 0.2624 RANDOM 42.241
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] 0.82 0.82 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.671 r_dihedral_angle_4_deg 22.268 r_dihedral_angle_3_deg 18.375 r_dihedral_angle_1_deg 8.266 r_scangle_it 5.641 r_scbond_it 3.834 r_mcangle_it 2.551 r_angle_refined_deg 2.478 r_mcbond_it 1.677 r_nbtor_refined 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.671 r_dihedral_angle_4_deg 22.268 r_dihedral_angle_3_deg 18.375 r_dihedral_angle_1_deg 8.266 r_scangle_it 5.641 r_scbond_it 3.834 r_mcangle_it 2.551 r_angle_refined_deg 2.478 r_mcbond_it 1.677 r_nbtor_refined 0.34 r_nbd_refined 0.278 r_symmetry_hbond_refined 0.267 r_symmetry_vdw_refined 0.243 r_xyhbond_nbd_refined 0.235 r_chiral_restr 0.159 r_bond_refined_d 0.029 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6043 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing