7STT

Crystal structure of sulfatase from Pedobacter yulinensis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	2.4 M sodium malonate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.62	α = 90
b = 83.62	β = 90
c = 116.052	γ = 120

Symmetry
Space Group	P 32 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 EIGER X 16M		2021-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.6	40	95.7	0.068	0.068	0.079	0.024	0.996	35.25	10.6		59449		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	67.5		0.449	0.449	0.487	0.186	0.859	2	5.8

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	6UST	1.603	39.366	59345	3033	95.528	0.149	0.1476	0.1779	22.307

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]
0.348	0.174		0.348		-1.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.706
r_dihedral_angle_4_deg	16.984
r_dihedral_angle_3_deg	12.265
r_dihedral_angle_1_deg	5.968
r_lrange_it	5.55
r_lrange_other	5.387
r_scangle_it	3.548
r_scangle_other	3.547
r_angle_other_deg	2.361
r_scbond_it	2.29
r_scbond_other	2.289
r_mcangle_it	2.156
r_mcangle_other	2.156
r_angle_refined_deg	1.842
r_mcbond_it	1.445
r_mcbond_other	1.443
r_symmetry_nbd_refined	0.253
r_symmetry_xyhbond_nbd_refined	0.237
r_nbd_refined	0.223
r_symmetry_nbd_other	0.213
r_nbd_other	0.213
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.147
r_symmetry_metal_ion_refined	0.127
r_metal_ion_refined	0.119
r_chiral_restr	0.105
r_xyhbond_nbd_other	0.104
r_symmetry_nbtor_other	0.076
r_bond_other_d	0.035
r_gen_planes_other	0.02
r_bond_refined_d	0.014
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3501
Nucleic Acid Atoms
Solvent Atoms	555
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-3000	data scaling
MOLREP	phasing