8YHI

The Crystal Structure of SHP1 from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HJP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M Hepes pH7.5, 2% PEG 400, 2.0M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.302	α = 90
b = 56.498	β = 90
c = 110.258	γ = 90

Symmetry
Space Group	P 21 2 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 EIGER X 9M		2023-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95373	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.75	45.3	99.9	0.088	16.4	13.4		29341

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78			0.975

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	1.75	39.488	29270	1420	99.836	0.194	0.1925	0.2266	30.129

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]
-1.927			1.386		0.541

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.518
r_dihedral_angle_3_deg	10.294
r_dihedral_angle_1_deg	6.321
r_lrange_it	5.234
r_lrange_other	5.183
r_dihedral_angle_2_deg	4.274
r_scangle_it	3.539
r_scangle_other	3.538
r_mcangle_it	2.583
r_mcangle_other	2.582
r_scbond_it	2.137
r_scbond_other	2.137
r_mcbond_it	1.587
r_mcbond_other	1.586
r_angle_refined_deg	1.087
r_angle_other_deg	0.404
r_nbd_refined	0.2
r_symmetry_nbd_other	0.181
r_nbd_other	0.178
r_nbtor_refined	0.174
r_symmetry_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.127
r_xyhbond_nbd_refined	0.121
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.058
r_symmetry_xyhbond_nbd_other	0.027
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2254
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	18

Software

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