7YZU

Crystal structure of the sulfoquinovosyl binding protein SmoF complexed with SQMe


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7OFY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.3 M sodium acetate, 0.1 M BIS-TRIS (pH 5.5) and 35% PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.0138.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.27α = 90
b = 99.38β = 90
c = 53.76γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5947.3399.40.280.3020.1480.987.76.948233
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.591.620.6795.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE70FY1.5947.3348179242999.2340.2390.23770.266918.698
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]
-0.852.683-1.833
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.259
r_dihedral_angle_4_deg20.047
r_dihedral_angle_3_deg13.227
r_dihedral_angle_1_deg6.422
r_lrange_it3.919
r_lrange_other3.796
r_scangle_it2.611
r_scangle_other2.611
r_mcangle_it1.853
r_mcangle_other1.853
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.259
r_dihedral_angle_4_deg20.047
r_dihedral_angle_3_deg13.227
r_dihedral_angle_1_deg6.422
r_lrange_it3.919
r_lrange_other3.796
r_scangle_it2.611
r_scangle_other2.611
r_mcangle_it1.853
r_mcangle_other1.853
r_scbond_it1.784
r_scbond_other1.784
r_angle_refined_deg1.507
r_angle_other_deg1.383
r_mcbond_it1.265
r_mcbond_other1.264
r_nbd_refined0.214
r_nbd_other0.19
r_symmetry_xyhbond_nbd_refined0.181
r_symmetry_nbd_other0.18
r_nbtor_refined0.167
r_xyhbond_nbd_refined0.158
r_symmetry_nbd_refined0.1
r_chiral_restr0.076
r_symmetry_nbtor_other0.076
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2915
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing