3BZF

The human non-classical major histocompatibility complex molecule HLA-E


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.329319% PEG 3350, 0.3M NaCl, 0.1M Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6553.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.52α = 90
b = 62.301β = 106.15
c = 98.769γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C

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
12.5500.09812.232033
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)
2.52.5650.3442.72065

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 REPLACEMENTTHROUGHOUT1MHE2.529.630365162098.590.203740.200180.26936RANDOM30.031
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]
0.59-2.55-1.94-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.081
r_dihedral_angle_4_deg25.71
r_dihedral_angle_3_deg17.02
r_scangle_it6.884
r_scbond_it6.824
r_dihedral_angle_1_deg4.917
r_mcangle_it4.765
r_mcbond_it4.252
r_angle_refined_deg2.354
r_angle_other_deg1.264
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.081
r_dihedral_angle_4_deg25.71
r_dihedral_angle_3_deg17.02
r_scangle_it6.884
r_scbond_it6.824
r_dihedral_angle_1_deg4.917
r_mcangle_it4.765
r_mcbond_it4.252
r_angle_refined_deg2.354
r_angle_other_deg1.264
r_mcbond_other1.065
r_symmetry_vdw_other0.303
r_nbd_other0.254
r_nbd_refined0.253
r_xyhbond_nbd_refined0.21
r_nbtor_refined0.209
r_symmetry_hbond_refined0.196
r_symmetry_vdw_refined0.195
r_chiral_restr0.153
r_nbtor_other0.108
r_xyhbond_nbd_other0.053
r_bond_refined_d0.034
r_gen_planes_refined0.013
r_bond_other_d0.008
r_gen_planes_other0.003
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6266
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement