7UJV

Structure of PHD2 in complex with HIF2a-CODD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5L9B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	32.5% (w/v) PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
1.7	27.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.078	α = 90
b = 37.597	β = 90
c = 42.148	γ = 90

Symmetry
Space Group	P 21 21 2

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 16M		2021-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97933	NSLS-II	17-ID-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.8	129.08	100	0.117	0.126	0.047	0.998	8.4	7.1		19834			20.58

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	100		0.79	0.86	0.334	0.695	0.8	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5L9B	1.8	42.183	19760	946	99.838	0.175	0.173	0.2134	Random	29.036

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]
-0.715			-0.482		1.198

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.087
r_dihedral_angle_3_deg	15.24
r_dihedral_angle_4_deg	14.35
r_dihedral_angle_1_deg	7.198
r_lrange_it	6.248
r_lrange_other	6.23
r_scangle_it	4.837
r_scangle_other	4.835
r_mcangle_it	3.078
r_mcangle_other	3.076
r_scbond_it	3.023
r_scbond_other	3.022
r_mcbond_it	2.037
r_mcbond_other	2.037
r_angle_refined_deg	1.368
r_angle_other_deg	0.461
r_symmetry_nbd_refined	0.272
r_nbd_refined	0.235
r_nbd_other	0.223
r_symmetry_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.066
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1888
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	18

Software

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