9IFT | pdb_00009ift

FSP1 (tetrapod ancestor) bound to FAD and NAD+

X-RAY DIFFRACTION

---

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	7.5	293	0.06 M MgCl2, 0.06 CaCl2, 0.1 M HEPES/MOPS (acid) pH 7.5, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.947	α = 90
b = 80.528	β = 100.69
c = 60.918	γ = 90

Symmetry
Space Group	P 1 21 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 4M		2023-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.873128	ESRF	MASSIF-3

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	1.45	48.09	99	0.096	0.104	0.038	0.999	10	6.9		72942

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	1.45	1.47		99.5	1.995	2.164	0.822	0.455		6.7

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	1.45	48.09	70631	2276	98.87	0.17656	0.1757	0.1809	0.2035	0.2075	RANDOM	20.486

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]
0.32		-1.11	-0.99		1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.065
r_dihedral_angle_2_deg	10.862
r_dihedral_angle_1_deg	6.67
r_long_range_B_refined	6.503
r_long_range_B_other	6.407
r_scangle_other	5.205
r_scbond_it	3.427
r_scbond_other	3.426
r_mcangle_other	2.758
r_mcangle_it	2.756
r_mcbond_it	1.925
r_mcbond_other	1.912
r_angle_refined_deg	1.663
r_angle_other_deg	0.547
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
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	2759
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	111

Software

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