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)
Type	Source	Accession Code	Details
experimental model	PDB	3BP7	PDB ENTRY 3BP7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	23% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.41

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH	Mirrors	2006-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.95373	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.85	50	95.8	0.08	12.41	3.1		38830

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)	Redundancy	Number Unique Reflections (All)
1	1.85	1.92	83.7		0.311	0.311	3.08	2.7	3323

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3BP7	1.85	46.63	38786	1929	95.83	0.175	0.173	0.222	RANDOM	20.192

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.221
r_dihedral_angle_4_deg	15.494
r_dihedral_angle_3_deg	13.27
r_dihedral_angle_1_deg	6.711
r_scangle_it	4.385
r_scbond_it	3.144
r_mcangle_it	1.942
r_angle_refined_deg	1.823
r_mcbond_it	1.725
r_angle_other_deg	0.931
r_mcbond_other	0.38
r_symmetry_vdw_other	0.359
r_symmetry_hbond_refined	0.243
r_nbd_refined	0.213
r_nbd_other	0.206
r_xyhbond_nbd_refined	0.198
r_symmetry_vdw_refined	0.186
r_chiral_restr	0.116
r_nbtor_other	0.09
r_bond_refined_d	0.022
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3159
Nucleic Acid Atoms
Solvent Atoms	502
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling