7STV | pdb_00007stv

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	5.5	295	0.1 M sodium citrate pH 5.5, 20% w/v polyethylene glycol 3000

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.728	α = 90
b = 82.728	β = 90
c = 115.292	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	2.34	40	98.8	0.101	0.101	0.148	0.048	0.998	18.5	9.2		19275

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	2.34	2.38	98.7		0.489	0.489	0.525	0.175	0.948	2	6.7

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	2.35	34.232	19228	943	98.353	0.174	0.1717	0.18	0.2295	0.22	56.402

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]
2.062	1.031		2.062		-6.691

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.863
r_dihedral_angle_4_deg	17.733
r_dihedral_angle_3_deg	13.266
r_dihedral_angle_1_deg	6.423
r_lrange_other	5.183
r_lrange_it	5.182
r_scangle_it	3.163
r_scangle_other	3.162
r_mcangle_it	2.86
r_mcangle_other	2.86
r_scbond_it	1.864
r_scbond_other	1.853
r_mcbond_it	1.719
r_mcbond_other	1.719
r_angle_refined_deg	1.313
r_angle_other_deg	1.271
r_nbd_other	0.28
r_symmetry_nbd_refined	0.242
r_symmetry_xyhbond_nbd_refined	0.224
r_nbd_refined	0.208
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.151
r_metal_ion_refined	0.141
r_symmetry_xyhbond_nbd_other	0.113
r_symmetry_nbtor_other	0.079
r_symmetry_metal_ion_refined	0.067
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3448
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	18

Software

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