3LV3 | pdb_00003lv3

Crystal structure of HLA-B*2705 complexed with a peptide derived from the human voltage-dependent calcium channel alpha1 subunit (residues 513-521)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A83	PDB ENTRY 2A83

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	20%(w/v) PEG 8000, 150mM NaCl, 20mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.29	α = 90
b = 54.614	β = 99.33
c = 69.834	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 4		2004-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.94	20		0.113	16.2		18393	31104

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	1.97			0.36	4.8		1529

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 2A83	1.94	19.46	28960	1544	98.12	0.17802	0.17553	0.17	0.22435	0.23	RANDOM	27.115

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]
0.15		0.37	-0.06		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.015
r_dihedral_angle_3_deg	13.98
r_dihedral_angle_4_deg	13.565
r_dihedral_angle_1_deg	5.754
r_scangle_it	3.208
r_scbond_it	1.915
r_angle_refined_deg	1.259
r_mcangle_it	1.224
r_mcbond_it	0.642
r_chiral_restr	0.093
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	3187
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	18

Software

Software
Software Name	Purpose
DNA	data collection
EPMR	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling