9MEF | pdb_00009mef

Conformational flexibility in HLA-B8: peptide tuning structural and dynamical changes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelPDB-Dev 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29815% PEG4000, 0.1m citrate acid pH5.4, 0.2M ammonium acetate
Crystal Properties
Matthews coefficientSolvent content
2.4750.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.75α = 90
b = 81.304β = 90
c = 110.504γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAGILENT ATLAS CCD2024-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE VMXi0.976254DiamondVMXi

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2765.491000.1140.9977.37.177999
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.271.4391.70.4834

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.2765.4974060393964.460.198230.196660.20650.226910.2367RANDOM22.972
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.634
r_long_range_B_other9.044
r_long_range_B_refined9.038
r_dihedral_angle_2_deg7.45
r_dihedral_angle_1_deg6.624
r_scangle_other6.57
r_scbond_it4.113
r_scbond_other4.112
r_mcangle_it3.868
r_mcangle_other3.868
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.634
r_long_range_B_other9.044
r_long_range_B_refined9.038
r_dihedral_angle_2_deg7.45
r_dihedral_angle_1_deg6.624
r_scangle_other6.57
r_scbond_it4.113
r_scbond_other4.112
r_mcangle_it3.868
r_mcangle_other3.868
r_mcbond_it2.428
r_mcbond_other2.428
r_angle_refined_deg1.729
r_angle_other_deg0.637
r_chiral_restr0.097
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3060
Nucleic Acid Atoms
Solvent Atoms300
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling