3HPB | pdb_00003hpb

Crystal structure of SNX5-PX domain in P212121 space group

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	277	the protein solution in the final superdex-75 buffer (20 mM Tris.HCl, 100 mM NaCl, 0.02% NaN3, pH 8.0) was concentrated to 8 mg/ml. The Se-Met derivative and the 2.19 A crystals were obtained using an optimized initial crystallization condition of 8 ul of protein vs 1 ul of reservoir solution (0.2M (NH4)2SO4, 0.1M Sodium cacodylate tryhydrate pH 6.5, 30% PEG 8000) at 4C by sitting drop vapor diffusion, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.39	59.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.957	α = 90
b = 75.874	β = 90
c = 77.512	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	RIGAKU SATURN 944	MIRRORS	2006-10-17	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	ROSENBAUM-ROCK MONOCHROMATOR HIGH-RESOLUTION DOUBLE-CRYSTAL SI(220) SAGITTAL FO CUSING, ROSENBAUM- ROCK VERTICAL FOCUSING MIRROR	2008-11-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT
2	SYNCHROTRON	APS BEAMLINE 22-ID	0.9793,0.9795,0.9718	APS	22-ID

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	2.19	28.78	93.4	0.033	28.1	4.18		12680		3

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)
	2.19	2.27	62.3		0.256	3.5	2.05

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	MAD	THROUGHOUT	2.19	28.78	11436	1244	93.3	0.24	0.236	0.235	0.284	0.2815	RANDOM	48.12

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]
-1.19			0.15		1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.298
r_dihedral_angle_4_deg	23.943
r_dihedral_angle_3_deg	16.213
r_dihedral_angle_1_deg	5.259
r_scangle_it	3.663
r_scbond_it	2.156
r_mcangle_it	1.324
r_angle_refined_deg	1.284
r_mcbond_it	0.682
r_chiral_restr	0.101
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
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	1274
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	1

Software

Software
Software Name	Purpose
StructureStudio	data collection
SnB	phasing
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling