3L3J

Crystal structure of HLA-B*4402 in complex with the F3A/R5A double mutant of a self-peptide derived from DPA*0201


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M6OPDB ENTRY 1M6O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.1M tri-sodium citrate dihydrate, 12-30% PEG 4000, 0.2M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5752.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.802α = 90
b = 82.214β = 90
c = 110.034γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2003-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
12.44184.80.1055.32.6169781697811
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)
12.42.587.30.2752

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1M6O2.441151221512265584.520.235230.235230.232980.28874RANDOM21.287
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]
-1.07-2.13.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.191
r_dihedral_angle_3_deg17.172
r_dihedral_angle_4_deg15.612
r_dihedral_angle_1_deg6.3
r_scangle_it2.171
r_scbond_it1.371
r_angle_refined_deg1.298
r_mcangle_it0.793
r_mcbond_it0.427
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.191
r_dihedral_angle_3_deg17.172
r_dihedral_angle_4_deg15.612
r_dihedral_angle_1_deg6.3
r_scangle_it2.171
r_scbond_it1.371
r_angle_refined_deg1.298
r_mcangle_it0.793
r_mcbond_it0.427
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3150
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms4

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling