9IKA | pdb_00009ika

Crystal structure of the tetrapyrrole binding domain in CoaR

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		289	(NH4)2SO4, Tris, PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.365	α = 90
b = 101.5	β = 90
c = 48.653	γ = 90

Symmetry
Space Group	P 21 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 S 9M		2024-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97881	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.26	34.58	98.4	0.104	0.11	0.035	0.995	15.9	9.6		22245			29.59

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.26	2.34	87.1		0.83	0.997	0.533	0.22	3.5	3.5

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	2.26	34.56	22197	1076	98.009	0.193	0.1921	0.2006	0.2097	0.2127	34.602

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]
1.195			-2.278		1.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.522
r_dihedral_angle_3_deg	12.582
r_lrange_it	6.15
r_lrange_other	6.077
r_dihedral_angle_1_deg	5.868
r_dihedral_angle_2_deg	4.946
r_scangle_it	4.124
r_scangle_other	4.123
r_mcangle_it	3.204
r_mcangle_other	3.203
r_scbond_it	2.336
r_scbond_other	2.336
r_mcbond_it	1.882
r_mcbond_other	1.881
r_angle_refined_deg	1.114
r_angle_other_deg	0.396
r_nbd_other	0.2
r_nbd_refined	0.187
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.157
r_symmetry_nbd_refined	0.131
r_xyhbond_nbd_refined	0.128
r_symmetry_xyhbond_nbd_refined	0.11
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.053
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2639
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	12

Software

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