3LQZ

Crystal Structure of HLA-DP2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529320% PEG4000, 300mM Sodium Chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.8674.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.2823α = 90
b = 157.2823β = 90
c = 61.8048γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray170CCDADSC QUANTUM 315MSINGLE WAVELENGTH
21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0ALS8.2.2
2SYNCHROTRONAPS BEAMLINE 19-ID1.0APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.25136.081007.11205322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.253.28389.16

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.25501133264586.160.218650.216930.25094RANDOM93.721
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]
5.942.975.94-8.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.92
r_dihedral_angle_3_deg21.43
r_dihedral_angle_4_deg20.275
r_dihedral_angle_1_deg6.719
r_scangle_it1.661
r_angle_refined_deg1.49
r_scbond_it0.957
r_mcangle_it0.672
r_mcbond_it0.364
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.92
r_dihedral_angle_3_deg21.43
r_dihedral_angle_4_deg20.275
r_dihedral_angle_1_deg6.719
r_scangle_it1.661
r_angle_refined_deg1.49
r_scbond_it0.957
r_mcangle_it0.672
r_mcbond_it0.364
r_nbtor_refined0.319
r_nbd_refined0.228
r_symmetry_vdw_refined0.221
r_xyhbond_nbd_refined0.182
r_chiral_restr0.096
r_symmetry_hbond_refined0.079
r_bond_refined_d0.012
r_gen_planes_refined0.004
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 Atoms3114
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms42

Software

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