6OBY | pdb_00006oby

The nucleotide-binding protein AF_226 in complex with ADP from Archaeoglobus fulgidus with Co found by PIXE. Based on 3KB1.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	PROTEIN SOLUTION: 100MM NACL, 5MM DTT, 0.02% NAN3, 10MM TRIS-HCL (PH 7.5). RESERVOIR SOLUTION: 100 MM NAACETATE (PH 4.6), 30% MPD, AND 200 MM NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.44	α = 90
b = 67.682	β = 90.09
c = 79.403	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	MAR CCD 165 mm	MIRRORS	2009-10-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.97899	NSLS	X4C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.8	30	98.3	0.093	0.076	15	3.5		26385

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	88.1		0.254	0.22		2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.87	28.54	11606	587	96.72	0.22036	0.21711	0.23	0.28395	0.29	RANDOM	49.987

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]
-7.61		-0.23	3.81		3.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.446
r_dihedral_angle_3_deg	17.641
r_dihedral_angle_4_deg	14.221
r_long_range_B_refined	9.97
r_long_range_B_other	9.97
r_dihedral_angle_1_deg	7.592
r_scangle_other	5.728
r_mcangle_it	5.26
r_mcangle_other	5.259
r_scbond_it	3.5
r_scbond_other	3.5
r_mcbond_it	3.268
r_mcbond_other	3.268
r_angle_refined_deg	1.434
r_angle_other_deg	1.138
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3764
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	55

Software

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