8PDI

The phosphatase and C2 domains of SHIP1 with covalent Z1763271112

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	41.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.498	α = 90
b = 78.993	β = 90
c = 89.289	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)	R Merge I (Observed)	Rpim I (All)	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	1.3	62.5	100	0.096	0.04	1	11.6	12.7		109198

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	100		0.998	0.581	0.7	12.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.3	59.163	109094	2038	99.983	0.147	0.146	0.1905	19.077

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]
-0.198			0.299		-0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.066
r_dihedral_angle_3_deg	13.41
r_dihedral_angle_2_deg	12.829
r_dihedral_angle_1_deg	7.283
r_rigid_bond_restr	4.64
r_lrange_it	4.137
r_lrange_other	3.84
r_scangle_it	2.963
r_scangle_other	2.963
r_dihedral_angle_other_3_deg	2.826
r_mcangle_it	2.568
r_mcangle_other	2.568
r_scbond_it	2.106
r_scbond_other	2.105
r_mcbond_it	1.887
r_mcbond_other	1.883
r_angle_refined_deg	1.779
r_angle_other_deg	0.626
r_dihedral_angle_other_2_deg	0.32
r_symmetry_nbd_refined	0.217
r_symmetry_xyhbond_nbd_other	0.206
r_nbd_refined	0.201
r_symmetry_nbd_other	0.196
r_nbd_other	0.187
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.17
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
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	532
Heterogen Atoms	25

Software

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