☰ Navigation Tabs
Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with LCMV-derived gp33 index peptide and three of its escape variants
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N5A PDB entry 1N5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.11 60.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.245 α = 90 b = 123.302 β = 103.13 c = 99.299 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 2003-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.097 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.9 84507 84423 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 99.8
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 1N5A 2.4 19.84 84507 82684 1684 99.99 0.246 0.20008 0.19915 0.2134 0.24611 0.2571 RANDOM 23.962
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] -0.03 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.416 r_scangle_it 2.963 r_scbond_it 1.776 r_angle_refined_deg 1.491 r_angle_other_deg 1.414 r_mcangle_it 1.292 r_mcbond_it 0.683 r_symmetry_vdw_other 0.275 r_nbd_other 0.243 r_nbd_refined 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.416 r_scangle_it 2.963 r_scbond_it 1.776 r_angle_refined_deg 1.491 r_angle_other_deg 1.414 r_mcangle_it 1.292 r_mcbond_it 0.683 r_symmetry_vdw_other 0.275 r_nbd_other 0.243 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.201 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.165 r_chiral_restr 0.092 r_nbtor_other 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12618 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing