8TK3 | pdb_00008tk3

HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) having oxidized catalytic cysteine and complexed with 6-(difluoromethyl)pyrimidin-4-ol at two allosteric sites

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		294	The protein in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA was mixed with the crystallization buffer (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000) and equilibrated against the crystallization buffer. The crystals were soaked with 25 mM of the compound in solution (10% DMSO, 100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000).

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.133	α = 90
b = 52.467	β = 90
c = 100.493	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 EIGER X 9M		2023-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9201	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.95	50.3	99	0.13	0.99	7.8	6.4		13585

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.18	96.1		0.68	0.91	2.7	7

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	2	40.25	12090	632	99.45	0.18968	0.18617	0.196	0.25538	0.2667	RANDOM	31.256

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]
-2.83			4.85		-2.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.846
r_dihedral_angle_2_deg	9.46
r_long_range_B_refined	8.299
r_long_range_B_other	8.271
r_dihedral_angle_1_deg	6.579
r_scangle_other	5.908
r_mcangle_other	4.141
r_mcangle_it	4.138
r_scbond_it	3.899
r_scbond_other	3.896
r_mcbond_it	2.768
r_mcbond_other	2.768
r_angle_refined_deg	1.593
r_angle_other_deg	0.518
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	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	1393
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	32

Software

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