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Crystal structure of HLA-B*4402 in complex with the F3A mutant of a self-peptide derived from DPA*0201
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6O PDB ENTRY 1M6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1M tri-sodium citrate dihydrate, 12-30% PEG 4000, 0.2M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.57 52.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.687 α = 90 b = 82.019 β = 90 c = 110.44 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 IMAGE PLATE RIGAKU RAXIS IV++ 2003-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
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 1.8 65.9 99.1 0.076 7 3.7 43106 43106 1 1
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 1.8 1.9 99.1 0.331 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1M6O 1.8 40.17 41479 41479 1742 99.39 0.18945 0.18945 0.18773 0.23112 0.2042 RANDOM 22.774
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] -0.23 -0.72 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.961 r_dihedral_angle_4_deg 18.098 r_dihedral_angle_3_deg 12.808 r_dihedral_angle_1_deg 6.237 r_scangle_it 4.412 r_scbond_it 2.852 r_mcangle_it 2.024 r_angle_refined_deg 1.385 r_mcbond_it 1.183 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.961 r_dihedral_angle_4_deg 18.098 r_dihedral_angle_3_deg 12.808 r_dihedral_angle_1_deg 6.237 r_scangle_it 4.412 r_scbond_it 2.852 r_mcangle_it 2.024 r_angle_refined_deg 1.385 r_mcbond_it 1.183 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3156 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 10
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling