7QHV | pdb_00007qhv

Crystal structure of the sulfoquinovosyl binding protein SmoF complexed with sulfoquinovosyl diacylglycerol

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7QHU	D_1292119394

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	279	0.2M L-Na-glutamate, alanine, glycine, lysine hydrochloride, serine, 0.1M TRIS, bicine, 12.5% MPD, PEG1000, PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.215	α = 90
b = 69.589	β = 91.539
c = 104.574	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	210	PIXEL	DECTRIS PILATUS 6M-F		2019-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97933	Diamond	I04

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	2.14	69.59	99.9	0.093	0.124	0.081	0.992	8.9	4.1		42301

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.14	2.2			0.305	0.406	0.265	0.942		4.1

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	D_1292119394	2.14	57.995	42277	2124	99.865	0.206	0.2035	0.21	0.2598	0.27	24.287

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]
3.124		3.128	-0.769		-2.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.392
r_dihedral_angle_4_deg	22.688
r_dihedral_angle_3_deg	14.801
r_dihedral_angle_1_deg	6.61
r_lrange_it	4.222
r_lrange_other	4.204
r_scangle_it	2.884
r_scangle_other	2.883
r_mcangle_it	2.553
r_mcangle_other	2.553
r_scbond_it	1.887
r_scbond_other	1.885
r_mcbond_other	1.677
r_mcbond_it	1.676
r_angle_refined_deg	1.504
r_angle_other_deg	1.3
r_symmetry_xyhbond_nbd_refined	0.214
r_nbd_refined	0.201
r_symmetry_nbd_other	0.179
r_nbd_other	0.173
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.155
r_symmetry_nbd_refined	0.111
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.043
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5828
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	73

Software

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