2RFX

Crystal Structure of HLA-B*5701, presenting the self peptide, LSSPVTKSF


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H6PPDB ENTRY 2H6P

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.4950.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.844α = 90
b = 49.029β = 100.7
c = 70.666γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.56094.30.08118.8315096
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.689.80.3125.13

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2H6P2.527.481397873595.750.212390.209480.26845RANDOM38.131
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]
2.640.86-1.52-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.553
r_dihedral_angle_3_deg16.549
r_dihedral_angle_4_deg16.178
r_dihedral_angle_1_deg5.479
r_scangle_it1.159
r_angle_refined_deg1.026
r_scbond_it0.683
r_mcangle_it0.465
r_nbtor_refined0.3
r_mcbond_it0.271
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.553
r_dihedral_angle_3_deg16.549
r_dihedral_angle_4_deg16.178
r_dihedral_angle_1_deg5.479
r_scangle_it1.159
r_angle_refined_deg1.026
r_scbond_it0.683
r_mcangle_it0.465
r_nbtor_refined0.3
r_mcbond_it0.271
r_symmetry_hbond_refined0.187
r_nbd_refined0.181
r_symmetry_vdw_refined0.165
r_xyhbond_nbd_refined0.114
r_chiral_restr0.074
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3127
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms24

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling