3BP7 | pdb_00003bp7

The high resolution crystal structure of HLA-B*2709 in complex 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	1JGE	PDB ENTRY 1JGE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	23.5% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.195	α = 90
b = 83.002	β = 90
c = 110.779	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	2006-01-18	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	1.79	50	93.3	0.057	19.4	3.6		41600			19.9

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	1.79	1.85	84.3		0.331	3.07	3.3	3694

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1JGE	1.8	46.08	41552	2090	92.85	0.169	0.167	0.18	0.204	0.21	RANDOM	14.028

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.206
r_dihedral_angle_4_deg	16.717
r_dihedral_angle_3_deg	12.653
r_dihedral_angle_1_deg	6.356
r_scangle_it	3.887
r_scbond_it	2.815
r_angle_refined_deg	1.631
r_mcangle_it	1.628
r_mcbond_it	1.506
r_angle_other_deg	1.128
r_symmetry_vdw_other	0.306
r_mcbond_other	0.305
r_nbd_refined	0.215
r_nbd_other	0.204
r_xyhbond_nbd_refined	0.149
r_symmetry_hbond_refined	0.142
r_chiral_restr	0.107
r_symmetry_vdw_refined	0.104
r_nbtor_other	0.086
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3161
Nucleic Acid Atoms
Solvent Atoms	513
Heterogen Atoms	6

Software

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