8Q5A | pdb_00008q5a

Crystal structure of metal-dependent class II sulfofructosephosphate aldolase from Hafnia paralvei HpSqiA-Zn in complex with dihydroxyacetone phosphate (DHAP)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8Q58

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	A crystal of the DHAP complex grew from 14 mg mL-1 enzyme in 50 mM Tris buffer pH 7.4 in a drop with 0.15 uL protein to 0.15 uL mother liquor soaked with SFP for 2 min, with the reservoir solution containing 25% PEG 1,500 w/v, 0.1 M SPG (succinic acid, propionate, glycine) buffer pH 7

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.605	α = 90
b = 87.669	β = 90
c = 103.3	γ = 90

Symmetry
Space Group	I 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 PILATUS 2M		2020-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	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	2.8	34.22	99.9	0.101	0.105	0.029	0.997	17.7	12.7		7522

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	2.8	2.95		100	0.439	0.456	0.123	0.971		13.4

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	2.8	34	7129	382	99.75	0.21133	0.20793	0.21	0.27408	0.27	RANDOM	46.956

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]
-1.51			2.32		-0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.757
r_long_range_B_refined	9.023
r_long_range_B_other	9.021
r_mcangle_other	7.019
r_mcangle_it	7.018
r_scangle_other	6.413
r_dihedral_angle_1_deg	6.224
r_dihedral_angle_2_deg	4.952
r_mcbond_it	4.547
r_mcbond_other	4.547
r_scbond_it	4.209
r_scbond_other	4.199
r_angle_refined_deg	1.251
r_angle_other_deg	0.447
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
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	1932
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	12

Software

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