6XY7 | pdb_00006xy7

Human SHIP1 with magnesium and phosphate bound to the active site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OKM

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, pH 6.5, 20 % PEG 500 MME, 10% PEG 20,000

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.5	α = 90
b = 79.088	β = 90
c = 89.255	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		2019-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.8266	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.086	59.193	87.6	0.152	0.155	0.03	0.998	11.7	26.9		159826

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.093	1.14	59.6		2.19	2.246	0.48	0.601	1.4	20.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	5OKM	1.086	59.193	159810	1775	85.905	0.136	0.1358	0.14	0.1587	0.16	14.339

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]
0.079			-0.008		-0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.754
r_dihedral_angle_4_deg	25.458
r_dihedral_angle_3_deg	12.711
r_dihedral_angle_1_deg	7.442
r_lrange_it	3.416
r_lrange_other	3.283
r_scangle_it	2.709
r_scangle_other	2.708
r_mcangle_other	2.483
r_mcangle_it	2.481
r_scbond_it	2.127
r_scbond_other	2.127
r_rigid_bond_restr	1.901
r_mcbond_it	1.889
r_mcbond_other	1.881
r_angle_refined_deg	1.702
r_angle_other_deg	1.465
r_symmetry_nbd_refined	0.223
r_nbd_other	0.222
r_nbd_refined	0.213
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3704
Nucleic Acid Atoms
Solvent Atoms	489
Heterogen Atoms	28

Software

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