3NR8 | pdb_00003nr8

Crystal structure of human SHIP2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I9Y	PDB ENTRY 1I9Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	20% PEG 6000, 0.1M citric acid pH 5, 2mM biphenyl 2,3',4,5',6-pentakisphosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.796	α = 90
b = 61.177	β = 91.9
c = 114.32	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	RAYONIX MX-225	mirrors	2010-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	44.77	99.6	0.152	0.152	7.9	4.6	15400	15338			59.7

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	2.95	99.5		0.72	0.72	2	4.6	2227

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1I9Y	2.8	20	14621	14524	755	99.34	0.21644	0.21644	0.21358	0.2158	0.27247	0.2723	RANDOM	35.337

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]
-0.68		2.19	-0.38		1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.215
r_dihedral_angle_4_deg	18.752
r_dihedral_angle_3_deg	16.575
r_dihedral_angle_1_deg	6.288
r_scangle_it	1.201
r_angle_refined_deg	1.146
r_angle_other_deg	0.807
r_scbond_it	0.702
r_mcangle_it	0.471
r_mcbond_it	0.245
r_chiral_restr	0.065
r_mcbond_other	0.046
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4784
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling