8TK2 | pdb_00008tk2

HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) complexed with 2-((2,4-difluorobenzyl)amino)-2-oxoacetic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VHR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	Protein-compound mixture in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA, 5% DMSO were mixed with the precipitant solution (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000) and equilibrated against the precipitant solution.

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.536	α = 78.07
b = 44.328	β = 89.99
c = 59.863	γ = 81.69

Symmetry
Space Group	P 1

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 PILATUS 6M		2022-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

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	1.7	38.69	89.4	0.049	8.8	2		34755

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	1.7	1.73	80.9		0.229	2.7	1.9

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	38.69	32683	2065	89.31	0.1786	0.17587	0.19	0.22265	0.24	RANDOM	29.235

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]
0.75	-1.78	0.41	1.04	-0.55	-2.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.507
r_dihedral_angle_2_deg	7.042
r_long_range_B_refined	6.891
r_long_range_B_other	6.859
r_dihedral_angle_1_deg	5.802
r_scangle_other	5.327
r_mcangle_it	3.981
r_mcangle_other	3.981
r_scbond_it	3.522
r_scbond_other	3.521
r_mcbond_it	2.771
r_mcbond_other	2.761
r_angle_refined_deg	1.43
r_angle_other_deg	0.486
r_chiral_restr	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2804
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	41

Software

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