9IFW | pdb_00009ifw

FSP1 (tetrapod ancestor) bound to FAD and NAD+ and compound 4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9IFT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.06 M MgCl2, 0.06 M CaCl2, 0.1 M imidazole/MES monohydrate (acid) pH 6.5, 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.66	α = 90
b = 79.51	β = 98.79
c = 112.785	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 PILATUS3 6M		2025-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.96546	ESRF	MASSIF-1

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	1.74	42.52	97.1	0.104	0.131	0.079	0.994	5	2.4		75055

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	1.74	1.78		96.5	1.055	1.34	0.815	0.277		2.4

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	1.74	42.52	71265	3763	96.63	0.20706	0.20492	0.2154	0.24829	0.2577	RANDOM	24.862

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]
0.85		-0.39	-1.77		0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.431
r_dihedral_angle_3_deg	15.155
r_dihedral_angle_1_deg	7.042
r_long_range_B_refined	6.291
r_long_range_B_other	6.274
r_scangle_other	4.827
r_scbond_it	3.088
r_scbond_other	3.088
r_mcangle_it	3.053
r_mcangle_other	3.053
r_mcbond_it	2.098
r_mcbond_other	2.098
r_angle_refined_deg	1.528
r_angle_other_deg	0.501
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
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	5524
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	279

Software

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