5OHS | pdb_00005ohs

A GH31 family sulfoquinovosidase mutant D455N in complex with pNPSQ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		apo

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Protein stock at 45 mg/mL in the buffer of 50 mM NaPO4 and 500 mM NaCl is mixed with the precipitant of 0.2 M KSCN, 21% PEG3350, 0.1 M bis-Tris propane pH 6.5, at a ratio of 1.2: 1.

Crystal Properties
Matthews coefficient	Solvent content
2.5	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.2	α = 90
b = 169.19	β = 92.8
c = 169.69	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M-F		2016-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97951	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.97	75.77	99.8	0.0779	0.998	11.6	4.1		411803

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.02	100		0.965	0.558	1.4	4.2

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 (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	apo	1.97	75.77	411803	20006	99.75	0.182	0.181	0.19	0.2026	0.21	RANDOM	34.7035

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]
-0.12		0.19	-1.03		1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.813
r_dihedral_angle_4_deg	18.044
r_dihedral_angle_3_deg	14.038
r_dihedral_angle_1_deg	6.399
r_angle_other_deg	3.798
r_angle_refined_deg	1.871
r_mcangle_it	1.629
r_mcbond_it	1.043
r_mcbond_other	1.038
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.813
r_dihedral_angle_4_deg	18.044
r_dihedral_angle_3_deg	14.038
r_dihedral_angle_1_deg	6.399
r_angle_other_deg	3.798
r_angle_refined_deg	1.871
r_mcangle_it	1.629
r_mcbond_it	1.043
r_mcbond_other	1.038
r_chiral_restr	0.122
r_bond_refined_d	0.018
r_gen_planes_other	0.017
r_gen_planes_refined	0.01
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	41583
Nucleic Acid Atoms
Solvent Atoms	2168
Heterogen Atoms	368

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
Coot	model building
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.