☰ Navigation Tabs
Crystal structure of HLA-B*4402 in complex with the F3A/R5A double 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 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.802 α = 90 b = 82.214 β = 90 c = 110.034 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++ 2003-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 2.4 41 84.8 0.105 5.3 2.6 16978 16978 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 2.4 2.5 87.3 0.275 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1M6O 2.4 41 15122 15122 655 84.52 0.23523 0.23523 0.23298 0.2326 0.28874 0.2951 RANDOM 21.287
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] -1.07 -2.1 3.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.191 r_dihedral_angle_3_deg 17.172 r_dihedral_angle_4_deg 15.612 r_dihedral_angle_1_deg 6.3 r_scangle_it 2.171 r_scbond_it 1.371 r_angle_refined_deg 1.298 r_mcangle_it 0.793 r_mcbond_it 0.427 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.191 r_dihedral_angle_3_deg 17.172 r_dihedral_angle_4_deg 15.612 r_dihedral_angle_1_deg 6.3 r_scangle_it 2.171 r_scbond_it 1.371 r_angle_refined_deg 1.298 r_mcangle_it 0.793 r_mcbond_it 0.427 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3150 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 4
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling