1KJM

TAP-A-associated rat MHC class I molecule


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52902M (NH4)2SO4, 1% glycerol, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.9658.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.049α = 90
b = 109.566β = 90
c = 45.3γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1999-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.08SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.3519.894.90.0812.72.7622313-332.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.43920.4231.862.382120

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 1ED3 MOLECULE 12.3519.821660215697.160.249350.24730.26803RANDOM11.686
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]
-1.125.96-4.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.483
r_dihedral_angle_1_deg3.077
r_scangle_it1.978
r_angle_refined_deg1.463
r_scbond_it1.126
r_angle_other_deg0.783
r_symmetry_hbond_refined0.751
r_mcangle_it0.614
r_mcbond_it0.319
r_nbd_other0.252
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.483
r_dihedral_angle_1_deg3.077
r_scangle_it1.978
r_angle_refined_deg1.463
r_scbond_it1.126
r_angle_other_deg0.783
r_symmetry_hbond_refined0.751
r_mcangle_it0.614
r_mcbond_it0.319
r_nbd_other0.252
r_nbd_refined0.249
r_symmetry_vdw_other0.249
r_xyhbond_nbd_other0.217
r_symmetry_vdw_refined0.192
r_xyhbond_nbd_refined0.176
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbtor_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3149
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms5

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement