3BXN

The high resolution crystal structure of HLA-B*1402 complexed with a Cathepsin A signal sequence peptide, pCatA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BVN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	24- 27%(w/v) PEG 20000, with 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.791	α = 90
b = 82.144	β = 90
c = 110.734	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	2007-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	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	1.864	50	96.8	0.07	20.14	4.6	38358	38358

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.864	1.93			0.24	3.6		3022

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	3BVN	1.864	50	2	38358	36391	1918	97.15	0.17181	0.16931	0.21904	RANDOM	20.459

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]
0.45			-0.92		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.422
r_dihedral_angle_4_deg	19.748
r_dihedral_angle_3_deg	14.144
r_dihedral_angle_1_deg	5.93
r_scangle_it	3.997
r_scbond_it	2.508
r_mcangle_it	1.558
r_angle_refined_deg	1.441
r_mcbond_it	0.975
r_nbtor_refined	0.303
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.153
r_chiral_restr	0.113
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3153
Nucleic Acid Atoms
Solvent Atoms	551
Heterogen Atoms	24

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling