3KYN

Crystal structure of HLA-G presenting KGPPAALTL peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.827718% PEG 3350, 0.2M potassium formate, 0.1M HEPES, 10mM cobalt chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.957.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.874α = 90
b = 76.874β = 90
c = 151.851γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-04-03MSINGLE 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
12.437.30.06124.42037838.01
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)
12.42.490.4162.8

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 REPLACEMENTTHROUGHOUT1YDP2.437.2719333104597.510.220890.216890.29913RANDOM44.309
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]
-0.02-0.01-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.675
r_dihedral_angle_3_deg16.595
r_dihedral_angle_4_deg16.131
r_dihedral_angle_1_deg6.729
r_scangle_it5.403
r_scbond_it4.039
r_mcangle_it2.328
r_mcbond_it1.915
r_angle_refined_deg1.406
r_angle_other_deg0.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.675
r_dihedral_angle_3_deg16.595
r_dihedral_angle_4_deg16.131
r_dihedral_angle_1_deg6.729
r_scangle_it5.403
r_scbond_it4.039
r_mcangle_it2.328
r_mcbond_it1.915
r_angle_refined_deg1.406
r_angle_other_deg0.935
r_mcbond_other0.341
r_symmetry_vdw_other0.215
r_nbd_refined0.201
r_nbd_other0.201
r_metal_ion_refined0.189
r_xyhbond_nbd_refined0.182
r_nbtor_refined0.176
r_symmetry_vdw_refined0.154
r_chiral_restr0.091
r_nbtor_other0.086
r_symmetry_hbond_refined0.079
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3138
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms3

Software

Software
Software NamePurpose
HKL-2000data collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing