6JP3

Crystal structure of peptide in complex with HLA-A1101.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X7Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52890.2M Sodium malonate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.0760.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.502α = 90
b = 90.525β = 90
c = 91.24γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.6664.27990.070.9512.47.264100
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.7030.8580.824

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1X7Q1.6664.2660966315398.970.167020.165560.19421RANDOM18.409
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]
-0.140.23-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.083
r_dihedral_angle_4_deg15.389
r_dihedral_angle_3_deg14.322
r_long_range_B_other7.893
r_long_range_B_refined7.889
r_dihedral_angle_1_deg6.372
r_scangle_other5.747
r_scbond_it3.765
r_scbond_other3.741
r_mcangle_it3.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.083
r_dihedral_angle_4_deg15.389
r_dihedral_angle_3_deg14.322
r_long_range_B_other7.893
r_long_range_B_refined7.889
r_dihedral_angle_1_deg6.372
r_scangle_other5.747
r_scbond_it3.765
r_scbond_other3.741
r_mcangle_it3.091
r_mcangle_other3.09
r_angle_refined_deg2.296
r_mcbond_it2.113
r_mcbond_other2.113
r_angle_other_deg1.159
r_chiral_restr0.146
r_bond_refined_d0.026
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3131
Nucleic Acid Atoms
Solvent Atoms447
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing