9FCE | pdb_00009fce

BelI in complex with SAM from Streptomyces sp. UCK14

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-A0A1W6R583-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.2 M LiCl, 0.1 M TRIS, 20% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.43	α = 90
b = 165	β = 90
c = 165.67	γ = 90

Symmetry
Space Group	F 2 2 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 EIGER X 16M		2022-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.95	30	95.1	0.042	15.9	3.9		38727

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.05	97.4		0.573	2.2

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	1.95	30	36781	1936	95.09	0.17234	0.17031	0.18	0.20748	0.22	RANDOM	50.256

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]
-2.08			2.68		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	17.5
r_long_range_B_other	17.271
r_scangle_other	11.94
r_mcangle_it	11.318
r_mcangle_other	11.316
r_dihedral_angle_3_deg	11.284
r_scbond_it	7.77
r_scbond_other	7.769
r_mcbond_it	7.521
r_mcbond_other	7.517
r_dihedral_angle_1_deg	5.957
r_dihedral_angle_2_deg	4.824
r_rigid_bond_restr	2.404
r_angle_refined_deg	1.133
r_angle_other_deg	0.42
r_chiral_restr	0.058
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3268
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	66

Software

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