8Q57 | pdb_00008q57

Crystal structure of class II SFP aldolase from Yersinia aldovae (YaSqiA-Zn-SO4) with bound sulfate ions

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UCK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	Protein at 16 mg mL-1 in 50 mM NaPi, 300 mM NaCl buffer pH 7.4, using a drop containing 0.6 uL protein and 0.5 uL mother liquor, the latter comprising 1.5 M ammonium sulfate, 0.1 M NaCl, 0.1 M BIS-TRIS pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.734	α = 90
b = 87.525	β = 107.73
c = 104.312	γ = 90

Symmetry
Space Group	I 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 PILATUS3 2M		2020-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.7	61.5	100	0.073	0.079	0.03	0.999	12.9	7.1		85319

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	1.7	1.73		99.9	1.181	1.276	0.481	0.752		6.9

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	1.7	61.01	81063	4241	99.95	0.18579	0.18477	0.2	0.20522	0.21	RANDOM	28.012

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]
-1.35		0.06	-1.26		2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.32
r_dihedral_angle_2_deg	9.819
r_long_range_B_refined	6.851
r_long_range_B_other	6.85
r_dihedral_angle_1_deg	5.73
r_scangle_other	5.652
r_scbond_it	3.892
r_scbond_other	3.891
r_mcangle_it	3.619
r_mcangle_other	3.618
r_mcbond_it	2.846
r_mcbond_other	2.843
r_angle_refined_deg	1.511
r_angle_other_deg	0.52
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
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	4181
Nucleic Acid Atoms
Solvent Atoms	271
Heterogen Atoms	68

Software

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