8Q59 | pdb_00008q59

Crystal structure of metal-dependent class II sulfofructose phosphate aldolase from Yersinia aldovae in complex with sulfofructose phosphate (YaSqiA-Zn-SFP)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8Q57

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	enzyme in 50 mM NaPi buffer pH 7.4 soaked with SFP for 30 seconds in a drop with 0.1 uL protein- 0.2 uL mother liquor, with the reservoir solution containing 1.5 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 1% PEG 3,350

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.637	α = 90
b = 87.739	β = 110.66
c = 91.008	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 PILATUS 2M		2020-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97628	Diamond	I03

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	2	48.12	100	0.097	0.104	0.039	0.997	11.6	7		57013

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	2	2.05		100	0.772	0.832	0.309	0.821		7.1

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	2	48	54253	2688	99.85	0.18807	0.1869	0.2	0.21151	0.22	RANDOM	34.482

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]
1.14		0.68	-2.05		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.244
r_dihedral_angle_2_deg	12.337
r_long_range_B_refined	7.224
r_long_range_B_other	7.211
r_scangle_other	6.145
r_dihedral_angle_1_deg	5.855
r_mcangle_other	4.43
r_mcangle_it	4.429
r_scbond_it	4.291
r_scbond_other	4.28
r_mcbond_it	3.514
r_mcbond_other	3.514
r_angle_refined_deg	1.65
r_angle_other_deg	0.517
r_chiral_restr	0.075
r_bond_refined_d	0.01
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	4202
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
MOLREP	phasing