7STU | pdb_00007stu

Crystal structure of sulfatase from Pedobacter yulinensis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7STT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.15 M potassium bromide, 30% w/v polyethylene glycol monomethyl ether 2000

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.286	α = 90
b = 83.286	β = 90
c = 115.793	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	295	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	2.23	40	99.2	0.128	0.128	0.172	0.057	0.997	15.14	9.1		23149

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	2.23	2.27	99.6		0.907	0.907	0.858	0.339	0.738	2	6.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7STT	2.23	39.217	23020	1205	99.19	0.176	0.1738	0.18	0.2252	0.22	33.47

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]
1.13	0.565		1.13		-3.664

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.014
r_dihedral_angle_3_deg	12.44
r_dihedral_angle_4_deg	11.544
r_dihedral_angle_1_deg	6.433
r_lrange_it	6.29
r_lrange_other	6.134
r_scangle_it	1.901
r_scangle_other	1.901
r_mcangle_it	1.831
r_mcangle_other	1.831
r_angle_refined_deg	1.382
r_angle_other_deg	1.331
r_scbond_it	1.105
r_scbond_other	1.105
r_mcbond_it	1.042
r_mcbond_other	1.039
r_symmetry_nbd_refined	0.248
r_symmetry_metal_ion_refined	0.236
r_nbd_refined	0.209
r_nbd_other	0.196
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.164
r_metal_ion_refined	0.139
r_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_refined	0.1
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.067
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3495
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms	9

Software

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