☰ Navigation Tabs
Crystal structure of a Murine MHC class I H2-Db molecule in complex with a photocleavable peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WBX PDB ENTRY 1WBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING-DROP, VAPOR-DIFFUSION METHOD WITH A WELL SOLUTION OF 15% (W/V) PEG 8000, 0.05 M K/NA PHOSPHATE, 50-100 MM BETA-OCTYL-GLUCOPYRANOSIDE AND 0.1 M CACODYLATE AT PH 6.4.
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.24 α = 90 b = 103.87 β = 90.83 c = 168.81 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 ADSC CCD 2005-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2.65 20 96.6 0.08 9.7 2 50561
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WBX 2.65 19.66 48002 2558 96.9 0.237 0.234 0.2335 0.291 0.2863 RANDOM 47.84
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] 0.53 0.92 2.57 -3.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.274 r_dihedral_angle_3_deg 14.541 r_dihedral_angle_4_deg 12.842 r_dihedral_angle_1_deg 5.136 r_angle_refined_deg 0.895 r_angle_other_deg 0.73 r_scangle_it 0.372 r_scbond_it 0.242 r_mcangle_it 0.231 r_mcbond_it 0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.274 r_dihedral_angle_3_deg 14.541 r_dihedral_angle_4_deg 12.842 r_dihedral_angle_1_deg 5.136 r_angle_refined_deg 0.895 r_angle_other_deg 0.73 r_scangle_it 0.372 r_scbond_it 0.242 r_mcangle_it 0.231 r_mcbond_it 0.214 r_nbtor_refined 0.173 r_nbd_refined 0.164 r_nbd_other 0.161 r_symmetry_hbond_refined 0.144 r_symmetry_vdw_other 0.139 r_symmetry_vdw_refined 0.116 r_xyhbond_nbd_refined 0.105 r_nbtor_other 0.084 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12628 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing