6Y7Q | pdb_00006y7q

Crystal Structure of the N-terminal PAS domain from the hERG3 Potassium Channel

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	hERG3 PAS domain (15 mg/ml, in 50 mM NaCl, 1 mM TCEP in a 1:1 ratio with reservoir solution (0.1 M NaCl, 0.1 M HEPES pH=7.5, 1.6 M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
1.75	29.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.784	α = 90
b = 32.784	β = 90
c = 200.681	γ = 90

Symmetry
Space Group	P 43 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 PILATUS3 6M		2017-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9795	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.39	66.9	100	0.061	13.9	11.9656537283		23496

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	1.39	1.43			0.766

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4HQA	1.39	50.221	22170	1208	99.983	0.187	0.1843	0.2	0.2352	0.25	32.173

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]
-1.748			-1.748		3.496

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.003
r_dihedral_angle_4_deg	27.681
r_dihedral_angle_3_deg	18.961
r_rigid_bond_restr	18.195
r_scangle_it	9.461
r_scangle_other	9.454
r_lrange_it	9.05
r_lrange_other	9
r_scbond_it	7.991
r_scbond_other	7.985
r_dihedral_angle_1_deg	7.135
r_mcangle_it	5.435
r_mcangle_other	5.432
r_mcbond_it	4.598
r_mcbond_other	4.569
r_angle_refined_deg	2.234
r_angle_other_deg	1.646
r_symmetry_nbd_refined	0.665
r_nbd_other	0.618
r_symmetry_xyhbond_nbd_refined	0.301
r_symmetry_nbd_other	0.257
r_nbd_refined	0.236
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.124
r_symmetry_nbtor_other	0.093
r_bond_refined_d	0.02
r_gen_planes_refined	0.016
r_bond_other_d	0.01
r_gen_planes_other	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	937
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	14

Software

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