8PDJ | pdb_00008pdj

The phosphatase and C2 domains of SHIP1 with covalent Z56948267

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XY7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM MES/imidazole 20 % PEG 500 MME, 10% PEG 20,000

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.711	α = 90
b = 79.568	β = 90
c = 89.631	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	PIXEL	DECTRIS EIGER2 XE 16M		2021-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.4	51.4	100	0.998	9.6	12		88912

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	100		0.422	1.1	12

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.4	49.301	88830	1964	99.984	0.134	0.1326	0.13	0.1898	0.19	21.222

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]
0.032			0.661		-0.693

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.944
r_dihedral_angle_4_deg	21.016
r_dihedral_angle_3_deg	12.952
r_dihedral_angle_1_deg	7.418
r_lrange_it	6.272
r_lrange_other	6.147
r_scbond_it	5.659
r_scbond_other	5.658
r_scangle_it	5.409
r_scangle_other	5.408
r_mcangle_it	5.135
r_mcangle_other	5.134
r_mcbond_it	3.901
r_mcbond_other	3.89
r_rigid_bond_restr	3.105
r_angle_refined_deg	1.77
r_angle_other_deg	1.463
r_nbd_other	0.225
r_nbd_refined	0.22
r_symmetry_xyhbond_nbd_other	0.199
r_symmetry_nbd_refined	0.192
r_symmetry_nbd_other	0.19
r_symmetry_xyhbond_nbd_refined	0.187
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.171
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3721
Nucleic Acid Atoms
Solvent Atoms	493
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing