7QQI

Sucrose phosphorylase from Faecalibaculum rodentium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6S9V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	Protein was concentrated to 30 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 1 M Na citrate, 0.1 M Tris, pH 7.0, 0.2 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
1.95	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.798	α = 90
b = 94.409	β = 90
c = 104.772	γ = 90

Symmetry
Space Group	P 21 21 21

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 2M		2020-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	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	1.36	46	99.7	0.076	0.095	0.056	0.999	10.7	5		95834

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	1.36	1.38			1.27	1.583	0.933	0.45		5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	6S9V	1.36	46	95748	4844	99.564	0.151	0.1495	0.1853	16.554

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]
-0.567			-1.915		2.483

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.472
r_dihedral_angle_4_deg	14.923
r_dihedral_angle_3_deg	11.739
r_rigid_bond_restr	7.317
r_dihedral_angle_1_deg	6.556
r_lrange_it	3.062
r_lrange_other	2.805
r_scangle_it	2.46
r_scangle_other	2.46
r_scbond_it	2.036
r_scbond_other	2.035
r_mcangle_other	1.714
r_mcangle_it	1.711
r_angle_other_deg	1.421
r_mcbond_it	1.372
r_angle_refined_deg	1.364
r_mcbond_other	1.357
r_nbd_refined	0.21
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.173
r_nbd_other	0.17
r_symmetry_xyhbond_nbd_refined	0.161
r_xyhbond_nbd_refined	0.136
r_symmetry_xyhbond_nbd_other	0.079
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3918
Nucleic Acid Atoms
Solvent Atoms	448
Heterogen Atoms	8

Software

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