12JS | pdb_000012js

Designed pentameric proton channel LQLL I13S

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MCT	PDB entry 6MCT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293	0.125 M CaCl2, 0.02 M TRIS pH 7.4, 30% PEG 3K, 30% PEG 400 Cryoprotectant

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.645	α = 90
b = 54.645	β = 90
c = 80.668	γ = 90

Symmetry
Space Group	P 42 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 EIGER2 XE 16M		2024-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-1	0.97946	SSRL	BL12-1

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	2.19	54.65	94.4	0.997	3.3	12.1		6350

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.19	2.26	82.3		5.315	0.4	10.1

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	2.9	45.242	2796	276	92.952	0.248	0.2445	0.2472	0.2775	0.2775	52.807

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]
0.182			0.182		-0.365

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.141
r_dihedral_angle_6_deg	13.749
r_lrange_it	12.366
r_dihedral_angle_2_deg	8.44
r_scangle_it	8.166
r_mcangle_it	7.613
r_scbond_it	5.115
r_mcbond_it	4.872
r_dihedral_angle_1_deg	3.77
r_angle_refined_deg	1.585
r_symmetry_nbd_refined	0.365
r_nbtor_refined	0.325
r_nbd_refined	0.219
r_chiral_restr	0.118
r_ncsr_local_group_3	0.115
r_ncsr_local_group_6	0.11
r_ncsr_local_group_10	0.109
r_ncsr_local_group_8	0.107
r_ncsr_local_group_7	0.106
r_ncsr_local_group_4	0.096
r_ncsr_local_group_1	0.094
r_ncsr_local_group_2	0.079
r_ncsr_local_group_9	0.077
r_ncsr_local_group_5	0.072
r_xyhbond_nbd_refined	0.06
r_gen_planes_refined	0.008
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1012
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	14

Software

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