8W0N

IRED crystal structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GEE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.1	295	Crystals were found in 20% PEG3350 with 200 mM sodium dihydrogen phosphate when set up in sitting drop plates with 200 nL reservoir and 200 nL of 12 mg/mL protein in SD-2 plates at room temperature.

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.844	α = 90
b = 127.698	β = 109.381
c = 63.598	γ = 90

Symmetry
Space Group	C 1 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	PIXEL	DECTRIS EIGER X 16M		2023-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.37	48.5	99.6	0.1	0.023	0.998	17.6	20.3		102543

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.37	1.39	92.7		0.985	0.233	0.914	3.9	18

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.37	48.5	102507	5158	99.597	0.12	0.1188	0.1438	16.548

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]
0.688		-0.523	0.899		-0.977

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.792
r_dihedral_angle_3_deg	14.491
r_dihedral_angle_1_deg	5.873
r_dihedral_angle_2_deg	5.663
r_rigid_bond_restr	4.256
r_lrange_it	2.966
r_lrange_other	2.953
r_scangle_other	2.327
r_scangle_it	2.326
r_scbond_it	1.745
r_scbond_other	1.745
r_angle_refined_deg	1.667
r_mcangle_it	1.552
r_mcangle_other	1.552
r_mcbond_it	1.238
r_mcbond_other	1.229
r_angle_other_deg	0.575
r_nbd_refined	0.23
r_nbd_other	0.213
r_symmetry_nbd_other	0.192
r_symmetry_nbd_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.08
r_ncsr_local_group_1	0.06
r_dihedral_angle_other_2_deg	0.023
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3894
Nucleic Acid Atoms
Solvent Atoms	462
Heterogen Atoms	104

Software

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