8Y0V

HIF prolyl hydroxylase 2 in complex with inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2M Ammonium phosphate monobasic, 0.1M Tris (8.3 8.7), 40% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.415	α = 90
b = 82.415	β = 90
c = 63.472	γ = 120

Symmetry
Space Group	P 63

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 PILATUS3 6M		2024-01-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9785	SSRF	BL18U1

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	2.5	47.43	99.9	0.98	9.2	7.2		8584

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	2.5	2.6			0.699

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	47.43	8578	410	99.825	0.228	0.2255	0.228	0.2907	0.2975	70

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]
0.977	0.488		0.977		-3.169

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	11.59
r_dihedral_angle_3_deg	10.195
r_dihedral_angle_1_deg	6.183
r_lrange_it	5.612
r_lrange_other	5.572
r_dihedral_angle_2_deg	4.2
r_mcangle_it	3.678
r_mcangle_other	3.676
r_scangle_it	3.448
r_scangle_other	3.446
r_mcbond_other	2.218
r_mcbond_it	2.217
r_scbond_it	2.085
r_scbond_other	2.062
r_angle_refined_deg	0.744
r_angle_other_deg	0.269
r_nbd_other	0.204
r_nbd_refined	0.197
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.177
r_symmetry_nbd_refined	0.167
r_xyhbond_nbd_refined	0.128
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.035
r_chiral_restr_other	0.022
r_bond_refined_d	0.004
r_gen_planes_refined	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	1558
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	37

Software

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