9IPL | pdb_00009ipl

A tetrapyrrole binding domain variant of CoaR in closed conformation at 2.28 angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	289	Bis-Tris, (NH4)2SO4, PEG3350

Crystal Properties
Matthews coefficient	Solvent content
4.24	73.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.043	α = 90
b = 96.043	β = 90
c = 148.664	γ = 120

Symmetry
Space Group	P 61

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 S 9M		2024-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.9788	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.28	49.57	100	0.095	1	20.5	20.1		35426			48.17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.28	2.34	100		1.755	0.791	2.3

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	2.28	45.74	33586	1733	99.79	0.20987	0.20884	0.2148	0.22974	0.2321	RANDOM	51.452

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]
0.2	0.1		0.2		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.528
r_long_range_B_other	10.189
r_long_range_B_refined	10.181
r_scangle_other	7.464
r_mcangle_it	6.246
r_mcangle_other	6.245
r_dihedral_angle_1_deg	5.807
r_dihedral_angle_2_deg	4.811
r_scbond_it	4.805
r_scbond_other	4.535
r_mcbond_it	4.073
r_mcbond_other	4.071
r_angle_refined_deg	1.27
r_angle_other_deg	0.461
r_chiral_restr	0.065
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2943
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	40

Software

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