2IXG | pdb_00002ixg

Crystal structure of the ATPase domain of TAP1 with ATP (S621A, G622V, D645N mutant)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6		SITTING DROP VAPOR DIFFUSION WITH A RESERVOIR CONTAINING 1.5 M SODIUM MALONATE PH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.477	α = 90
b = 67.477	β = 90
c = 105.903	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	277	IMAGE PLATE	RIGAKU IMAGE PLATE	MIRRORS	2005-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	2.7	40	99.4	0.14	11.3	4.6		7168		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	2.7	2.8	100		0.44	3.7	4.9

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 2IXE	2.7	26.47	6424	709	99.7	0.217	0.212	0.22	0.267	0.26	RANDOM	28.85

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]
0.28			0.28		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.013
r_dihedral_angle_3_deg	10.193
r_dihedral_angle_4_deg	9.561
r_dihedral_angle_1_deg	4.22
r_angle_refined_deg	0.79
r_angle_other_deg	0.725
r_scangle_it	0.313
r_scbond_it	0.188
r_symmetry_hbond_refined	0.179
r_nbtor_refined	0.162
r_nbd_other	0.155
r_nbd_refined	0.149
r_symmetry_vdw_other	0.148
r_mcangle_it	0.102
r_symmetry_vdw_refined	0.099
r_mcbond_it	0.091
r_xyhbond_nbd_refined	0.082
r_nbtor_other	0.078
r_chiral_restr	0.046
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_refined	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	1931
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	37

Software

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