8PDH | pdb_00008pdh

The phosphatase and C2 domains of SHIP1 with covalent Z1742148362

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
2.09	41.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.508	α = 90
b = 79.171	β = 90
c = 89.378	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	1.45	79.2	100	0.998	8	12.9		79287

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	1.45	1.47	100		0.453

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	1.45	51.276	79176	2097	99.95	0.146	0.144	0.15	0.2018	0.2	20.658

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]
-0.088			0.478		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.157
r_dihedral_angle_4_deg	22.961
r_dihedral_angle_3_deg	12.713
r_dihedral_angle_other_3_deg	8.335
r_dihedral_angle_1_deg	7.375
r_lrange_it	6.017
r_lrange_other	5.866
r_scangle_it	5.543
r_scangle_other	5.542
r_mcangle_it	4.903
r_mcangle_other	4.902
r_scbond_it	4.36
r_scbond_other	4.359
r_mcbond_it	3.841
r_mcbond_other	3.84
r_rigid_bond_restr	3.089
r_angle_refined_deg	1.753
r_angle_other_deg	1.455
r_nbd_refined	0.238
r_nbd_other	0.228
r_symmetry_nbd_refined	0.213
r_symmetry_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.195
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_other	0.102
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3704
Nucleic Acid Atoms
Solvent Atoms	482
Heterogen Atoms	29

Software

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