4IKB | pdb_00004ikb

Crystal structure of SNX11 PX domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	0.2M ammonium sulfate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30% PEG 8000, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.48	α = 90
b = 38.74	β = 101.13
c = 73.46	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		CCD	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9792	SSRF	BL17U

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	1.776	72.069	97.4	0.064	17.6	5.2	27836	27836

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.88	96.4		0.129	0.129	0.144	0.063	5.2	5.3	3973

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.78	34.12	27834	1407	97.04	0.1713	0.1687	0.1804	0.2213	0.1818	RANDOM	19.4674

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]
0.35		0.27	-0.09		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.794
r_dihedral_angle_4_deg	15.518
r_dihedral_angle_3_deg	13.332
r_dihedral_angle_1_deg	6.096
r_angle_refined_deg	1.732
r_angle_other_deg	0.942
r_chiral_restr	0.13
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2111
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	78

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BALBES	phasing