3BP7

The high resolution crystal structure of HLA-B*2709 in complex with a Cathepsin A signal sequence peptide, pCatA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JGEPDB ENTRY 1JGE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529123.5% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6353.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.195α = 90
b = 83.002β = 90
c = 110.779γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMirrors2006-01-18MSINGLE 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
11.795093.30.05719.43.64160019.9
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)
11.791.8584.30.3313.073.33694

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 1JGE1.846.0841552209092.850.1690.1670.204RANDOM14.028
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]
0.05-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.206
r_dihedral_angle_4_deg16.717
r_dihedral_angle_3_deg12.653
r_dihedral_angle_1_deg6.356
r_scangle_it3.887
r_scbond_it2.815
r_angle_refined_deg1.631
r_mcangle_it1.628
r_mcbond_it1.506
r_angle_other_deg1.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.206
r_dihedral_angle_4_deg16.717
r_dihedral_angle_3_deg12.653
r_dihedral_angle_1_deg6.356
r_scangle_it3.887
r_scbond_it2.815
r_angle_refined_deg1.631
r_mcangle_it1.628
r_mcbond_it1.506
r_angle_other_deg1.128
r_symmetry_vdw_other0.306
r_mcbond_other0.305
r_nbd_refined0.215
r_nbd_other0.204
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.142
r_chiral_restr0.107
r_symmetry_vdw_refined0.104
r_nbtor_other0.086
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3161
Nucleic Acid Atoms
Solvent Atoms513
Heterogen Atoms6

Software

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