9VSJ | pdb_00009vsj

Crystal structure of the genetically-encoded green calcium sensor icBTnC2 in its calcium bound-state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8YQ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		287	30% MPD,20mM CaCl2 ,100 mM NaAcetate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
3.59	65.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.697	α = 90
b = 128.697	β = 90
c = 52.737	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2025-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4	0.75172	KURCHATOV SNC	K4.4

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	1.55	55.73	99.9	0.973	6.7	12.9		72730

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	1.55	1.58			0.53	1.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.55	55.73	69063	3647	99.85	0.19847	0.19736	0.2069	0.21958	0.2283	RANDOM	23.069

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]
-0.09	-0.05		-0.09		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	14.002
r_dihedral_angle_3_deg	12.553
r_long_range_B_other	10.378
r_long_range_B_refined	10.374
r_scangle_other	9.411
r_dihedral_angle_1_deg	7.883
r_scbond_it	6.892
r_scbond_other	6.89
r_mcangle_it	6.035
r_mcangle_other	6.033
r_rigid_bond_restr	5.942
r_mcbond_it	4.309
r_mcbond_other	4.309
r_angle_refined_deg	1.913
r_angle_other_deg	1.034
r_chiral_restr	0.11
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.006
r_gen_planes_other	0.005
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2367
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	10

Software

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