3BP4

The high resolution crystal structure of HLA-B*2705 in complex with a Cathepsin A signal sequence peptide pCatA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BP7PDB ENTRY 3BP7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529123% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5852.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.161α = 90
b = 82.4β = 90
c = 109.846γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMirrors2006-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.95373BESSY14.2

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
11.855095.80.0812.413.138830
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9283.70.3110.3113.082.73323

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 3BP71.8546.6338786192995.830.1750.1730.222RANDOM20.192
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.221
r_dihedral_angle_4_deg15.494
r_dihedral_angle_3_deg13.27
r_dihedral_angle_1_deg6.711
r_scangle_it4.385
r_scbond_it3.144
r_mcangle_it1.942
r_angle_refined_deg1.823
r_mcbond_it1.725
r_angle_other_deg0.931
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.221
r_dihedral_angle_4_deg15.494
r_dihedral_angle_3_deg13.27
r_dihedral_angle_1_deg6.711
r_scangle_it4.385
r_scbond_it3.144
r_mcangle_it1.942
r_angle_refined_deg1.823
r_mcbond_it1.725
r_angle_other_deg0.931
r_mcbond_other0.38
r_symmetry_vdw_other0.359
r_symmetry_hbond_refined0.243
r_nbd_refined0.213
r_nbd_other0.206
r_xyhbond_nbd_refined0.198
r_symmetry_vdw_refined0.186
r_chiral_restr0.116
r_nbtor_other0.09
r_bond_refined_d0.022
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3159
Nucleic Acid Atoms
Solvent Atoms502
Heterogen Atoms12

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling