9I64 | pdb_00009i64

Crystal structure of Casdatifan bound to HIF2a-B*:ARNT-B* complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F1N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.10 M Sodium Acetate, 1.25 M Sodium Fluoride

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.693	α = 90
b = 61.15	β = 90
c = 91.32	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 16M		2021-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.999858	SLS	X06SA

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	1.558	45.76	99.6	0.999	13.9	8.1		42717

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	1.558	1.585			0.695

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	1.558	45.702	42716	3888	99.546	0.193	0.1914	0.2032	0.214	0.2253	23.743

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]
-1.491			2.236		-0.745

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	31.026
r_dihedral_angle_other_6_deg	15.736
r_dihedral_angle_6_deg	12.245
r_dihedral_angle_3_deg	11.76
r_dihedral_angle_1_deg	7.018
r_lrange_it	4.647
r_lrange_other	4.326
r_dihedral_angle_2_deg	2.084
r_mcangle_it	1.934
r_mcangle_other	1.934
r_scangle_it	1.894
r_scangle_other	1.894
r_angle_refined_deg	1.167
r_scbond_it	1.103
r_scbond_other	1.101
r_mcbond_it	1.085
r_mcbond_other	1.084
r_angle_other_deg	0.509
r_nbd_refined	0.193
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.167
r_nbd_other	0.146
r_symmetry_nbd_refined	0.127
r_symmetry_xyhbond_nbd_refined	0.075
r_symmetry_nbtor_other	0.073
r_xyhbond_nbd_refined	0.072
r_chiral_restr	0.061
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1772
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing