1W72 | pdb_00001w72

Crystal structure of HLA-A1:MAGE-A1 in complex with Fab-Hyb3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DUZ	PDB ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4
experimental model	PDB	7FAB	PDB ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4
experimental model	PDB	2GFB	PDB ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4
experimental model	PDB	2FB4	PDB ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		MES PH 6.5, NACL 600MM, 19% PEG3350, 80MM DIOXANE

Crystal Properties
Matthews coefficient	Solvent content
2.1	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.359	α = 90
b = 50.05	β = 109.85
c = 136.705	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	MARRESEARCH		2002-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	2.15	30	90	0.06	15	2.4		78453		2

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	2.15	2.23	90		0.23	2.3	2.2

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 ENTRIES 1DUZ, 7FAB, 2GFB, 2FB4	2.15	120	74477	3961	89.7	0.186	0.182	0.19	0.248	0.26	RANDOM	22.22

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]
-0.08		-0.79	-0.38		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.518
r_dihedral_angle_4_deg	14.169
r_dihedral_angle_3_deg	11.947
r_dihedral_angle_1_deg	4.482
r_scangle_it	2.908
r_scbond_it	2.036
r_angle_refined_deg	1.475
r_mcangle_it	1.374
r_mcbond_it	1.094
r_angle_other_deg	0.819
r_symmetry_vdw_other	0.233
r_symmetry_hbond_refined	0.218
r_symmetry_vdw_refined	0.211
r_nbd_refined	0.193
r_nbd_other	0.19
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.091
r_nbtor_refined	0.085
r_nbtor_other	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12794
Nucleic Acid Atoms
Solvent Atoms	653
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing