8RUV | pdb_00008ruv

HIF prolyl hydroxylase 2 (PHD2) T387I variant bound to Fe(III), 2-oxoglutarate (2OG) and Hypoxia-inducible Factor 2alpha (HIF2alpha)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		PHD2 bound to HIF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	(10-35%) PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6).

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.116	α = 90
b = 42.956	β = 90
c = 130.508	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 PILATUS 6M		2022-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.66	65.25	100	1	4.7	13.2		26202			20.68

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.66	1.69			0.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.66	65.25	1.33	25972	1285	99.27	0.239	0.238	0.2385	0.2572	0.2563	26.44

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.2803
f_angle_d	0.7554
f_chiral_restr	0.0483
f_plane_restr	0.0055
f_bond_d	0.0043

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1827
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	11

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.