7YZU | pdb_00007yzu

Crystal structure of the sulfoquinovosyl binding protein SmoF complexed with SQMe

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.3 M sodium acetate, 0.1 M BIS-TRIS (pH 5.5) and 35% PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.27	α = 90
b = 99.38	β = 90
c = 53.76	γ = 90

Symmetry
Space Group	P 21 21 21

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		2019-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.59	47.33	99.4	0.28	0.302	0.148	0.98	7.7	6.9		48233

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.59	1.62			0.679		5.6

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	70FY	1.59	47.33	48179	2429	99.234	0.239	0.2377	0.24	0.2669	0.27	18.698

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]
-0.85			2.683		-1.833

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.259
r_dihedral_angle_4_deg	20.047
r_dihedral_angle_3_deg	13.227
r_dihedral_angle_1_deg	6.422
r_lrange_it	3.919
r_lrange_other	3.796
r_scangle_it	2.611
r_scangle_other	2.611
r_mcangle_it	1.853
r_mcangle_other	1.853
r_scbond_it	1.784
r_scbond_other	1.784
r_angle_refined_deg	1.507
r_angle_other_deg	1.383
r_mcbond_it	1.265
r_mcbond_other	1.264
r_nbd_refined	0.214
r_nbd_other	0.19
r_symmetry_xyhbond_nbd_refined	0.181
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.158
r_symmetry_nbd_refined	0.1
r_chiral_restr	0.076
r_symmetry_nbtor_other	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2915
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	16

Software

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